<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