Document:

<PAGE>

                                                                    EXHIBIT 10.6

                              AMENDMENT NO. 2 TO
                             AMENDED AND RESTATED
                         REGISTRATION RIGHTS AGREEMENT

     THIS AMENDMENT NO. 2 TO AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT
(the "Second Amendment") is made and entered into as of the 7th day of January,
2000 by and among eDocs, Inc., a Delaware corporation (the "Company"), Kevin
Laracey, Kris Canekeratne and James Moran (each, a "Founder" and together, the
"Founders"), the holders of the Company's Series A Convertible Preferred Stock
(the "Series A Holders"), the holders of the Company's Series B Convertible
Preferred Stock (the "Series B Investors"), the holders of the Company's Series
C Convertible Preferred Stock (the "Series C Holders") and those persons or
entities listed as Purchasers (the "Series D Investors") on Exhibit 2.01A to
                                                            -------------
that certain Series D Convertible Preferred Stock Purchase Agreement of even
date herewith (the "Series D Purchase Agreement").  The Series A Holders, the
Series B Investors, the Series C Investors and the Series D Investors are
hereinafter referred to individually as an "Investor" and collectively as the
"Investors."

     WHEREAS, the Company, the Founders, the Series A Holders, the Series B
Investors, and the Series C Investors are parties to an Amended and Restated
Registration Rights Agreement dated as of April 30, 1999, as amended by
Amendment No. 1 dated as of August 6, 1999 (as so amended, the "Amended and
Restated Registration Rights Agreement").

     WHEREAS, the Series D Investors have on this date purchased, and the
Company has issued to the Series D Investors pursuant to the Series D Purchase
Agreement, the number of shares of the Company's Series D Convertible Preferred
Stock, $0.001 par value per share, as set forth opposite the Series D Investors'
respective names on Exhibit 2.01A to the Series D Purchase Agreement; and
                    -------------

     WHEREAS, it is a condition precedent to the obligation of the Series D
Investors under the Series D Purchase Agreement that the Company, the Series A
Holders, the Series B Investors and the Series C Investors amend the Amended and
Restated Registration Rights Agreement to admit the Series D Investors as
parties thereto;

     NOW, THEREFORE, in consideration of the mutual promises and covenants
contained in this Amendment and in the Series D Purchase Agreement and pursuant
to Section 13 of the Amended and Restated Registration Rights Agreement, the
Company and the Holders (as defined in the Amended and Restated Registration
Rights Agreement) holding at least sixty percent (60%) of the Registrable Stock
(as defined in the Amended and Restated Registration Rights Agreement) and the
securities convertible into, exchangeable for or exercisable for Registrable
Stock, do hereby amend the Amended and Restated Registration Rights Agreement,
as follows:
<PAGE>

                                      -2-

     1.  The definitions of "Investors" and "Preferred Stock" set forth in
Section 1 of the Amended and Restated Registration Rights Agreement shall each
be amended and restated as follows:

         "Investors" means the Series A Holders, the Series B Investors, the
          ---------
     Series C Investors, and the persons or entities which purchased or will
     purchase shares of Series D Preferred Stock pursuant to the Series D
     Purchase Agreement.

         "Preferred Stock" means the Series A Preferred Stock, the Series B
          ---------------
     Preferred Stock, the Series C Preferred Stock, and the Series D Preferred
     Stock, in each case, now owned or hereinafter acquired.

     2.  Section 1 of the Amended and Restated Registration Rights Agreement
shall be amended by adding the definitions of "Series C Investors", "Series D
Preferred Stock" and "Series D Purchase Agreement" as follows:

          "Series C Investors" shall mean and include those persons or entities
           ------------------
     which purchased shares of Series C Preferred Stock pursuant to the Series C
     Purchase Agreement.

          "Series D Preferred Stock" means the Company's Series D Convertible
           ------------------------
     Preferred Stock, $0.001 par value per share.

          "Series D Purchase Agreement" shall mean that certain Series D
           ---------------------------
     Convertible Preferred Stock Purchase Agreement dated as of January 7, 2000
     by and among the Company and those persons or entities listed on Exhibit
                                                                      -------
     2.01A thereto.
     -----

     3.   Section 20 of the Amended and Restated Registration Rights Agreement
shall be amended and restated as follows:

          20.  Additional Parties.  Each party hereto agrees that any person or
               ------------------
     entity who acquires any Series C Preferred Stock of the Company pursuant to
     the Series C Purchase Agreement and any person or entity who acquires any
     Series D Preferred Stock of the Company pursuant to the Series D Purchase
     Agreement may become a party to this Agreement by executing a counterpart
     hereto, in which event such person or entity shall become bound by and
     shall enjoy the benefits conferred hereby.

     4.   Governing Law.  This Second Amendment shall be governed by, construed
          -------------
in accordance with, the laws of the Commonwealth of Massachusetts (without
regard to conflict of laws provisions).

     5.   Entire Agreement.  The Amended and Restated Registration Rights
          ----------------
Agreement, as amended hereby, constitutes the full and entire understanding
among the parties regarding the subject matter herein. Except as otherwise
expressly provided herein,
<PAGE>

                                      -3-

the provisions hereof shall inure to the benefit of, and be binding upon, the
successors, assigns, heirs, executors and administrators of the parties hereto.

     6.   Full Force and Effect.  Except as amended hereby, the Amended and
          ---------------------
Restated Registration Rights Agreement shall remain in full force and effect.

     7.   Counterparts.  This Second Amendment may be executed in two or
          ------------
more counterparts, each of which shall be deemed an original, but all of which
together shall constitute one and the same instrument.

     8.   Headings.  Headings in this Second Amendment are included for
          --------
reference only and have no effect upon the construction or interpretation of any
part of this Second Amendment.

                 [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]
<PAGE>

                                      -4-

     IN WITNESS WHEREOF, the Company has caused this Second Amendment to be
executed by a duly authorized officer, and each Investor has duly executed this
Second Amendment (or has caused it to be executed by a duly authorized officer,
partner, trustee or agent, as the case may be), as of the date first above
recited.

                              COMPANY:

                              eDocs, Inc.

                              By:/s/ Kevin Laracey
                                 -----------------

                      (See counterpart signature pages.)
<PAGE>

                              AMENDMENT NO. 2 TO
                             AMENDED AND RESTATED
                         REGISTRATION RIGHTS AGREEMENT

                        * COUNTERPART SIGNATURE PAGE *
                          --------------------------

                          INVESTORS:
                          ---------

                          CHARLES RIVER PARTNERSHIP VIII,
                          A Limited Partnership

                          By:/s/ Jonathan M. Guerster
                             ------------------------
                          Address:  1000 Winter Street
                                    Suite 3300
                                    Boston, MA  02154

                          SIGMA PARTNERS IV, L.P.

                          By:/s/ Robert E. Davoli
                             --------------------
                          Address:  2884 Sand Hill Road, Suite 121
                                    Menlo Park, CA 94025

                          SIGMA ASSOCIATES IV, L.P.

                          By:/s/ Robert E. Davoli
                             --------------------
                          Address:  2884 Sand Hill Road, Suite 121
                                    Menlo Park, CA 94025

<PAGE>

                          SIGMA INVESTORS IV, L.P.

                          By:/s/ Robert E. Davoli
                             --------------------
                          Address:  2884 Sand Hill Road, Suite 121
                                    Menlo Park, CA 94025

                          SIGMA PARTNERS V, L.P.

                          By: /s/ Robert E. Davoli
                              --------------------
                          Address:  2884 Sand Hill Road, Suite 121
                                    Menlo Park, CA 94025

                          SIGMA ASSOCIATES V, L.P.

                          By:/s/ Robert E. Davoli
                             --------------------
                          Address:  2884 Sand Hill Road, Suite 121
                                    Menlo Park, CA 94025

                          SIGMA INVESTORS V, L.P.

                          By:/s/ Robert E. Davoli
                             --------------------
                          Address:  2884 Sand Hill Road, Suite 121
                                    Menlo Park, CA 94025

<PAGE>

                          JAFCO CO., LTD.

                          By:/s/ Barry J. Schiffman
                             ----------------------
                             Barry J. Schiffman, President
                             JAFCO America Ventures Inc.
                             Attorney-in-fact

                          Address:  One Boston Place
                                    Suite 3320
                                    Boston, MA  02108

                          JAFCO L-1 VENTURE CAPITAL
                          INVESTMENT LIMITED PARTNERSHIP

                          By: /s/ Barry J. Schiffman
                              ----------------------
                              Barry J. Schiffman, President
                              JAFCO America Ventures Inc.
                              Attorney-in-fact

                          Address:  One Boston Place
                                    Suite 3320
                                    Boston, MA  02108

                          JAFCO USIT FUND III, L.P.

                          By:  /s/ Barry J. Schiffman
                               ----------------------
                               Barry J. Schiffman, Executive Managing
                               Principal
                               JAV Management Associates III, L.L.C.
                               Its General Partner

                          Address:  One Boston Place
                                    Suite 3320
                                    Boston, MA  02108

<PAGE>

                          THE GOLDMAN SACHS GROUP, Inc.

                          By:  /s/ Joseph Gleberman
                               --------------------
                               Name:  Joseph G. Gleberman
                               Title:  Vice President

                          Address:  85 Broad Street, 10th Floor
                                    New York, NY  10004
                                    Attention: Tara Harrison

                          Facsimile:  (212) 357-5505

                          STONE STREET FUND 1999, L.P.
                          By:  Stone Street 1999, L.L.C.,
                               its general partner

                          By:/s/ Katherine L. Nissenbaum
                             ---------------------------
                             Name: Katherine L. Nissenbaum
                                   Title: Vice President

                          Address:  85 Broad Street, 10th Floor
                                    New York, NY  10004
                                    Attention:  Tara Harrison

                          Facsimile:  (212) 357-5505

                          COMDISCO, INC.

                          By:/s/ James Labe
                             --------------

                          Address:  6111 North River Road
                                    Rosemont, IL  60018

<PAGE>

                          GE CAPITAL EQUITY INVESTMENTS, INC.

                          By:/s/ Michael S. Fisher
                             ---------------------
                             Name:  Michael S. Fisher
                             Title:  Sr. Vice President

                          Address:  120 Long Ridge Road
                                    Stamford, CT  06927-5000

                          FOUNDERS:
                          --------

                          /s/ Kevin E. Laracey
                          --------------------
                          Kevin E. Laracey

                          /s/ James Moran
                          ---------------
                          James Moran

                          /s/ Kris Canekeratne
                          --------------------
                          Kris Canekeratne

<PAGE>

                             AMENDED AND RESTATED
                             --------------------
                         REGISTRATION RIGHTS AGREEMENT

                          Counterpart Signature Page

                            Dated January 31, 2000

          Reference is made to that certain Amended and Restated Registration
Rights Agreement dated as of April 30, 1999 by and among eDocs, Inc., a Delaware
corporation (the "Company") and the parties thereto, as amended by Amendment No.
1 dated as of August 6, 1999 and Amendment No. 2 dated January 7, 2000 (as so
amended, the "Registration Rights Agreement").  Capitalized terms used as
defined terms herein and not otherwise defined shall have the meanings ascribed
to such terms in the Registration Rights Agreement.

          Vignette Corporation (the "Additional Purchaser") has, on this date
purchased, and the Company has issued to the Additional Purchaser pursuant to
that certain Series D Convertible Preferred Stock Purchase Agreement dated as of
January 7, 2000 by and among the Company and the Persons listed on Exhibit 2.01A
                                                                   -------------
thereto, 156,646 shares of the Series D Convertible Preferred Stock, $0.001 par
value per share (the "Series D Preferred Stock"), of the Company.

          By execution of this Counterpart Signature Page to the Registration
Rights Agreement, the undersigned hereby:  (a) acknowledges receipt of a copy of
the Registration Rights Agreement; (b) agrees that the shares of Common Stock
issuable upon conversion of the Series D Preferred Stock acquired by the
undersigned shall be included within the meaning of Registrable Stock for all
purposes of, and shall be subject in all respects to, the Registration Rights
Agreement; and (c) agrees that the undersigned shall be bound by and obtain the
benefit of the rights and restrictions of the Registration Rights Agreement as a
Holder thereunder.

                 [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]
<PAGE>

              AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT

                          Counterpart Signature Page

          IN WITNESS WHEREOF, the parties hereto have hereunto set their hands
as of the date first above written.

                          COMPANY:
                          -------
                          eDocs, Inc.

                          By: /s/ Kevin E. Laracey
                              --------------------
                              Kevin E. Laracey
                              President

                          VIGNETTE CORPORATION

                          By: /s/ David Brodsky
                              -----------------
                              Name:
                              Title:<PAGE>

                                                                    EXHIBIT 10.7
                                                                    ------------
                              AMENDMENT NO. 3 TO
                             AMENDED AND RESTATED
                         REGISTRATION RIGHTS AGREEMENT
                                      AND
                         WAIVER OF REGISTRATION RIGHTS

     THIS AMENDMENT NO. 3 TO AMENDED AND RESTATED REGISTRATION RIGHTS AGREEMENT
(the "Third Amendment") and WAIVER OF REGISTRATION RIGHTS (the "Waiver") is made
and entered into as of the 22nd day of March, 2000 by and among edocs, Inc., a
Delaware corporation (the "Company"), Kevin Laracey, Kris Canekeratne and James
Moran (each, a "Founder" and together, the "Founders"), the holders of the
Company's Series A Convertible Preferred Stock (the "Series A Holders"), the
holders of the Company's Series B Convertible Preferred Stock (the "Series B
Holders"), the holders of the Company's Series C Convertible Preferred Stock
(the "Series C Holders") and the holders of the Company's Series D Convertible
Preferred Stock (the "Series D Holders").

     All capitalized terms used herein but not defined herein shall have the
respective meanings as set forth in the Amended and Restated Registration Rights
Agreement dated as of April 30, 1999, as amended by Amendment No. 1 dated as of
August 6, 1999 and Amendment No. 2 dated as of January 7, 2000 (as so amended,
the "Amended and Restated Registration Rights Agreement").

     WHEREAS, the Company, the Founders, the Series A Holders, the Series B
Holders, the Series C Holders and the Series D Holders are parties to the
Amended and Restated Registration Rights Agreement.

     WHEREAS, the Company and the Holders wish to amend the provisions of
Section 13 of the Amended and Restated Registration Rights Agreement as set
forth herein.

     WHEREAS, the Company is planning an underwritten public offering (the
"Proposed Offering") of its common stock, par value $0.001 per share (the
"Common Stock"), pursuant to a Registration Statement (the "Registration
Statement") which is expected to be filed with the Securities and Exchange
Commission.

     WHEREAS, in connection with the Proposed Offering, Goldman, Sachs & Co.,
FleetBoston Robertson Stephens Inc., and U.S. Bancorp Piper Jaffray Inc., as
representatives of the several underwriters (the "Underwriters"), have requested
that all holders of registration rights relating to the securities of the
Company which such holders may have with respect to the Proposed Offering waive
any and all such rights.

     NOW, THEREFORE, in consideration of the mutual promises and covenants
contained in this Third Amendment and pursuant to Section 13 of the Amended and
Restated Registration Rights Agreement, the Company and the Holders holding at
least sixty percent (60%) of the Registrable Stock and the securities
convertible into,
<PAGE>

                                      -2-

exchangeable for or exercisable for Registrable Stock (calculated on an as
converted, exchanged or exercised basis), do hereby amend the Amended and
Restated Registration Rights Agreement, as follows:

     1.   Section 13 of the Amended and Restated Registration Rights Agreement
shall be amended and restated as follows:

          13. Waivers; Amendments. No waiver of any right hereunder by any party
              -------------------
     shall operate as a waiver of any other right, or of the same right with
     respect to any subsequent occasion for its exercise, or of any right to
     damages. No waiver by any party of any breach of this Agreement shall be
     held to constitute a waiver of any other breach or a continuation of the
     same breach. All remedies provided by this Agreement are in addition to all
     other remedies provided by law. Except for Section 3, this Agreement may
     not be amended or modified, and no provision hereof may be waived, except
     by a writing executed by the Company and the Holders of at least sixty
     percent (60%) of the then outstanding Registrable Stock and the securities
     convertible into, exchangeable for or exercisable for Registrable Stock
     (calculated on an as converted, exchanged or exercised basis). Section 3
     may only be amended, modified or any provision thereof waived by a writing
     executed by the Company, the Holders of at least a majority of the Founder
     Registrable Stock and the Holders of at least sixty percent (60%) of the
     then outstanding Registrable Stock and the securities convertible into,
     exchangeable for or exercisable for Registrable Stock (calculated on an as
     converted, exchanged or exercised basis). This Agreement may be amended,
     modified or any provision hereof waived with the consent of the Holders
     holding less than all of the outstanding Registrable Stock or Founder
     Registrable Stock only in a manner which applies to all such Holders in the
     same fashion.

     2.  Waiver of Registration Rights.  In connection with the Proposed
         -----------------------------
Offering and as an inducement for the Underwriters to enter into an underwriting
agreement with the Company, pursuant to Section 13 of the Amended and Restated
Registration Rights Agreement, as amended by paragraph 1 hereof, the Holders
holding at least sixty percent (60%) of the Registrable Stock and the Holders
holding at least a majority of the Founder Registrable Stock hereby waive and
relinquish, on behalf of all Holders of Registrable Stock and Founder
Registrable Stock, any and all registration rights relating to the securities of
the Company which the Holders may have with respect to the Proposed Offering,
pursuant to the Amended and Restated Registration Rights Agreement, or under any
other contract, agreement, charter provision or otherwise binding on the
Company.  The Holders also waive, on behalf of all Holders of Registrable Stock
and Founder Registrable Stock, any notice period requirements with respect to
any such registration rights.  This waiver shall lapse and become null and void
if the Registration Statement shall not have been declared effective on or
before October 31, 2000.

     3.    Governing Law.  This Third Amendment and Waiver shall be governed by,
           -------------
construed in accordance with, the laws of the Commonwealth of Massachusetts
(without regard to conflict of laws provisions).
<PAGE>

                                      -3-

     4.    Entire Agreement.  The Amended and Restated Registration Rights
           ----------------
Agreement, as amended hereby, constitutes the full and entire understanding
among the parties regarding the subject matter herein.  Except as otherwise
expressly provided herein, the provisions hereof shall inure to the benefit of,
and be binding upon, the successors, assigns, heirs, executors and
administrators of the parties hereto.

     5.    Full Force and Effect.  Except as amended hereby, the Amended and
           ---------------------
Restated Registration Rights Agreement shall remain in full force and effect.

     6.    Counterparts.  This Third Amendment and Waiver may be executed in
           ------------
two or more counterparts, each of which shall be deemed an original, but all of
which together shall constitute one and the same instrument.

     7.    Headings.  Headings in this Third Amendment and Waiver are included
           --------
for reference only and have no effect upon the construction or interpretation of
any part of this Third Amendment and Waiver.

                  [REMAINDER OF PAGE INTENTIONALLY LEFT BLANK]
<PAGE>

                                      -4-

     IN WITNESS WHEREOF, the Company has caused this Third Amendment and Waiver
to be executed by a duly authorized officer, and each Holder has duly executed
this Third Amendment and Waiver (or has caused it to be executed by a duly
authorized officer, partner, trustee or agent, as the case may be), as of the
date first above recited.

                              COMPANY:

                              edocs, Inc.

                              By: /s/ Kevin Laracey
                                 ------------------

                      (See counterpart signature pages.)
<PAGE>

                                      -5-

                              AMENDMENT NO. 3 TO
                             AMENDED AND RESTATED
                         REGISTRATION RIGHTS AGREEMENT
                                      AND
                         WAIVER OF REGISTRATION RIGHTS

                        * COUNTERPART SIGNATURE PAGE *
                          --------------------------

                              INVESTORS:
                              ---------

                              CHARLES RIVER PARTNERSHIP VIII,
                              A Limited Partnership

                              By:/s/ Jonathan M. Guester
                                 -----------------------
                              Address:  1000 Winter Street
                                        Suite 3300
                                        Boston, MA  02154

                              SIGMA PARTNERS IV, L.P.

                              By:/s/ Robert E. Davoli
                                 --------------------
                              Address:  2884 Sand Hill Road, Suite 121
                                        Menlo Park, CA 94025

                              SIGMA ASSOCIATES IV, L.P.

                              By:/s/ Robert E. Davoli
                                 --------------------
                              Address:  2884 Sand Hill Road, Suite 121
                                        Menlo Park, CA 94025

<PAGE>

                                      -6-

                              SIGMA INVESTORS IV, L.P.

                              By:/s/ Robert E. Davoli
                                 --------------------
                              Address:  2884 Sand Hill Road, Suite 121
                                        Menlo Park, CA 94025

                              SIGMA PARTNERS V, L.P.

                              By:/s/ Robert E. Davoli
                                 --------------------
                              Address:  2884 Sand Hill Road, Suite 121
                                        Menlo Park, CA 94025

                              SIGMA ASSOCIATES V, L.P.

                              By:/s/ Robert E. Davoli
                                 --------------------
                              Address:  2884 Sand Hill Road, Suite 121
                                        Menlo Park, CA 94025

                              SIGMA INVESTORS V, L.P.

                              By:/s/Robert E. Davoli
                                 -------------------
                              Address:  2884 Sand Hill Road, Suite 121
                                        Menlo Park, CA 94025

<PAGE>

                                      -7-

                              JAFCO CO., LTD.

                              By:/s/ Andrew P. Goldfarb
                                 ----------------------
                                 Andrew P. Goldfarb, Managing Member
                                 JAV Management Associates III, LLC

                              Address:  One Boston Place
                                        Suite 3320
                                        Boston, MA  02108

                              JAFCO L-1 VENTURE CAPITAL
                              INVESTMENT LIMITED PARTNERSHIP

                              By:/s/ Andrew P. Goldfarb
                                 ----------------------
                                 Andrew P. Goldfarb, Managing Member
                                 JAV Management Associates III, LLC

                              Address:  One Boston Place
                                        Suite 3320
                                        Boston, MA  02108

                              JAFCO USIT FUND III, L.P.

                              By:/s/ Andrew P. Goldfarb
                                 ----------------------
                                 Andrew P. Goldfarb, Managing Member
                                 JAV Management Associates III, LLC

                              Address:  One Boston Place
                                        Suite 3320
                                        Boston, MA  02108
<PAGE>

                                      -8-

                              THE GOLDMAN SACHS GROUP, L.P.

                              By:  /s/ Terence M. O'Toole
                                   ----------------------
                                   Name: Terence M. O'Toole
                                   Title: Attorney-in-Fact

                              Address:  85 Broad Street, 10th Floor
                                        New York, NY  10004
                                        Attention:  Tara Harrison

                              Facsimile: (212) 357-5505

                              STONE STREET FUND 1999, L.P.
                              By:  Stone Street 1999, L.L.C.,
                              its general partner

                              By:/s/ John E. Bowman
                                 ------------------
                                 Name: John E. Bowman
                                 Title: Vice President

                              Address:  85 Broad Street, 10th Floor
                                        New York, NY  10004
                                        Attention:  Tara Harrison

                              Facsimile:  (212) 357-5505

                              COMDISCO, INC.

                              By:
                                 ------------------------

                              Address:  6111 North River Road
                                        Rosemont, IL  60018

<PAGE>

                                      -9-

                              AMERICAN EXPRESS TRAVEL RELATED SERVICES
                              COMPANY, INC.

                              By:
                                 --------------------------

                              Address:  American Express Tower
                                        World Financial Center
                                        New York, NY  10285

                              GE CAPITAL EQUITY INVESTMENTS, INC.

                              By:
                                 ----------------------------
                                 Name:  Michael S. Fisher
                                        Title:  Sr. Vice President

                              Address:  120 Long Ridge Road
                                        Stamford, CT  06927-5000

                              VIGNETTE CORPORATION

                              By:
                                 -----------------------------
                                 Name:  David Brodsky
                                        Title:  Vice President of Finance

                               Address:  901 South Mopac Expressway
                                         Austin, TX 78746

                               FOUNDERS:
                               --------

                               /s/ Kevin E. Laracey
                               ---------------------
                               Kevin E. Laracey

                               /s/ James Moran
                               ---------------------
                               James Moran

                               /s/ Kris Canekeratne
                               --------------------
                               Kris Canekeratne

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