<PAGE>   1
                                                                    EXHIBIT 10.6



                               September 18, 1997



Medaphis Corporation
2840 Mt. Wilkinson Parkway
Suite 300
Atlanta, Georgia 30339
Attn: David McDowell
      Chief Executive Officer

                    RE:  Second Amended and Restated Credit Agreement, dated as
                         of February 4, 1997 (the "Credit Agreement"), among
                         Medaphis Corporation (the "Borrower"), the lenders
                         signatory thereto (collectively, the "Lenders"),
                         and SunTrust Bank, Atlanta, as agent for the Lenders
                         (the "Agent")

Gentlemen:

          All capitalized terms used herein and not otherwise defined
 herein shall have the meanings given such terms in the Credit Agreement.

          You have requested that the Required Lenders (a) grant a
waiver of compliance with the financial covenants set forth in Section 7.09(a),
7.09(b), 7.09(c) and 7.09(d) of the Credit Agreement as of and for the periods
ending September 30, 1997, December 31, 1997 and March 31, 1998, and (b)
consent to the sale by Imonics Corporation of the excess equipment of such
Subsidiary described on  Exhibit A attached hereto (collectively, the
"Excess Imonics Equipment").

          The purpose of this letter is to confirm that, subject to the terms
and conditions of this letter, the Required Lenders hereby waive any
requirement under the Credit Agreement that the Borrower comply with any of the
covenants set forth in Section 7.09(a), 7.09(b), 7.09(c) or 7.09(d) of the
Credit Agreement as of and for the periods ending September 30, 1997, December
31, 1997 and March 31, 1998; provided however, that in consideration of such
waivers:

               (i)  Borrower shall pay to the Agent, on the effective date of
          this letter as provided below, a waiver fee (which fee shall be fully
          earned upon the effectiveness of this letter) in an amount equal to
          three-eighths of one percent (0.375%) of the aggregate Revolving Loan
          Commitments of all Lenders, and such fee shall be distributed by the 
          Agent to those Lenders who are signatories to this letter in 
          accordance with their respective pro rata shares thereof (based on
          the proportion that each signing Lender's Revolving Loan Commitment
          bears to the sum of all of
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               such signing Lenders' Revolving Loan Commitments - it being
               understood and agreed that Section 4.09 of the Credit Agreement
               shall not apply to such fee); and

                    (ii) Borrower also shall be obligated to cause all of the
               Lenders' Revolving Loan Commitments to be terminated and all
               Obligations owed to all Lenders for the payment of money (other
               than (X) indemnity obligations not yet due and payable and (y)
               Cash Management Services Obligations) to be paid in full by 
               November 30, 1997 (or such other date no later than June 30, 1998
               to which such deadline may be extended by the Required Lenders in
               their discretion), and any failure on the Borrower's part to 
               cause such termination and payment to occur by the applicable
               deadline shall constitute an Event of Default under Section
               9.01(v) of the Credit Agreement which may be waived or acted
               upon by the Required Lenders in their discretion in accordance
               with the terms and conditions of the Credit Agreement as amended
               and supplemented by this letter (it being understood and agreed
               that Section 11.08(a)(iv) of the Credit Agreement shall not 
               apply to any extension of the aforesaid deadline to a date which
               occurs on or before June 30, 1998 or any waiver of any Event of 
               Default arising from Borrower's failure to cause such
               termination and payment to occur by such deadline, and Section
               11.08(a)(iv) shall continue to apply to any extension of such
               dealine beyond June 30, 1998 or to any waiver of any Event of
               Default arising from Borrower's failure to cause such payment to
               occur by June 30, 1998).

               This Letter also confirms that, subject to the terms and
conditions of this letter, the Required Lenders hereby consent to the sale by
Imonics Corporation of the Excess Imonics Equipment (and all of the Lenders' and
the Agent's Liens on such Collateral under the Security Documents shall be
released upon the sale thereof), provided that (i) the Net Proceeds of such sale
are applied in accordance with Section 2.06 of the Credit Agreement (and,
pending such application, the Lenders' and the Agent's Liens shall attach
thereto pursuant to the Security Documents and such proceeds shall constitute
Collateral for the Obligations) and (ii) no Default or Event of Default exists
at the time of such sale.

               Please note that this letter (and the waivers and consent
confirmed herein) shall not become effective unless and until (a) the aforesaid
waiver fee has been paid and (b) this letter has been signed by the Required
Lenders and this letter has been accepted and agreed to by Borrower, in each
case by such person's signing a copy of this letter in the appropriate space
indicated below and returning the same to the Agent's counsel (which may be
done by telecopy and in counterparts).
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                  Please note that the waivers and consent confirmed in this
letter relate solely to the specific covenants, dates and time periods
described above and nothing in this letter is intended (or shall be construed)
to constitute a waiver of or a consent to a departure from any other covenants
in the Credit Agreement.

                                    SUNTRUST BANK, ATLANTA, as Agent
                                    and as a Lender


                                    By: /s/ R.E. Tincher
                                       -----------------------------------------
                                       Name: Robert E. Tincher
                                            ------------------------------------
                                       Title: SVP
                                             -----------------------------------


                                    By:  /s/ David H. Eidson
                                       -----------------------------------------
                                      Name:  David H. Eidson
                                           -------------------------------------
                                      Title:   SVP
                                            ------------------------------------

                                    THE CHASE MANHATTAN BANK, as a
                                    Lender


                                    By:  /s/ C.T. Moore
                                       -----------------------------------------
                                      Name:  C.T. Moore
                                           -------------------------------------
                                      Title:  Managing Director
                                            ------------------------------------

                                    CREDITANSTALT-BANKVEREIN, as a 
                                    Lender


                                    By:  /s/ John G. Taylor
                                       -----------------------------------------
                                      Name:  John G. Taylor
                                           -------------------------------------
                                      Title:  Senior Associate
                                            ------------------------------------

                                    By:  /s/ Stephen W. Hipp
                                       -----------------------------------------
                                      Name:  Stephen w. Hipp
                                           -------------------------------------
                                      Title:  Associate
                                            ------------------------------------

                                    NATIONSBANK, N.A., as a Lender


                                    By:  /s/ DeWitt W. King, III
                                       -----------------------------------------
                                      Name:  DeWitt W. King, III
                                           -------------------------------------
                                      Title:  Senior Vice President
                                            ------------------------------------
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                                    PNC BANK, N.A., as a Lender


                                    By:  /s/ Thomas J. McCool
                                       -----------------------------------------
                                      Name:  Thomas J. McCool
                                           -------------------------------------
                                      Title:  Senior Vice President
                                            ------------------------------------

                                    WACHOVIA BANK, N.A., as a Lender


                                    By:  /s/ Ann B. Edwards
                                       -----------------------------------------
                                      Name:  Ann B. Edwards
                                           -------------------------------------
                                      Title:  Assistant Vice President
                                            ------------------------------------


ACCEPTED AND AGREED TO
this 18th day of September, 1997:

MEDAPHIS CORPORATION


By:  /s/ Caryn Dickerson
   -----------------------------------------
  Name:  Caryn Dickerson
       -------------------------------------
  Title:  Treasurer
        ------------------------------------


cc:      Each Guarantor