There are a couple of ways to deal with merchant fees.
You may need to add a 6-XXXX merchant fee account in the general ledger first.
1.On the debtor's form, enter only what was received into the bank account. This will create a credit.
Add a debtor's adjustment down for the fee, using tax code G, and post to the 6-XXXX merchant fee account.
Allocate the credit to the outstanding value.
or
2.Receive the full payment.
Add a cheque entry out of the bank account for the fee and post to the 6-XXXX Merchant Fee account.
Reconcile the full payment with the merchant fee in the bank reconciliation.
Further information
Apply a Credit Card Charge Using Stock