Typically when I have a Credit Card payment, I add the credit card fees as an entry in the Apply to Revenues Tab to the proper expense and then receive it as one payment. This way the full transaction is together and when reconciling the checking account, I don't need to find both portions of the transaction.

Unfortunately when I have a prepayment on a Credit Card, you can't add a second line in the prepayment screen of the Receipts Journal. I did a General Journal entry to reflect the fees and lower the cash account by the amount of fees but I'm wondering if anyone knows if there is a setting or some way of allowing a second line item in the Prepayment portion of the Receipts Journal.