When you receive a check from a Vendor to cover credit balances in Accounts Payable, you will need to perform a couple of steps.
1. You will need to Delete the A/P Credits on the Vendor Account via Open Item Maintenance
2. Post the check in Post Customer Payments using Customer ID "NONE" and add comment describing reason for payment, and take to your G/L Account for COGS Material or to the same G/L Account from when the A/P Credit was posted. It needs to go in and out of the G/L.
NOTE: If both GL accounts used are flagged as a Bank Account in GL Account Inquiry, then both the Positive and Negative side of the transaction will show in your Customer Payment Register, one in each account. Both can be cleared from your Customer Payment Register and will flow to the appropriate account for Bank Reconciliation.