The credit memo, assuming you will enter an invoice number on the return, is really just a negative invoice that will get created by the return of goods update, but won't be "associated" with the original invoice. After the Return is updated (with an invoice number), when you go to pay the vendor, you'll just select both invoices.
Now, if you really want to affect the original invoice, what you could do is once the return update creates the negative invoice, use AP invoice data entry to adjust the negative invoice to 0 (adjust by a positive amount), and adjust the original invoice down (adjust by a negative amount) by the same amount. Use a suspense GL account on both adjustment invoice lines so the net effect to GL is 0.
Note if the original invoice and negative invoice result in 0 due the vendor, you can also use Manual Check Entry to Apply the two invoices (assuming you will never actually pay the vendor). To get help on this subject, select Manual Check Entry off AP's main menu, and click the help (?) icon. Select the topic "apply a credit memo to an invoice" for instructions.
Hope that helps.
