Receive the full sales amount (either Applied to an Invoice or directly to Revenue) and then add a line on the Apply to Revenue tab for the credit card fee and input the amount as a negative. Example: Invoice for $100 with a $4 credit card fee -- enter $100.00 receipt and it will credit your sales GL account, enter your ($4.00) and it will debit your credit card fee GL account and the balance of $96.00 will debit your cash account and tie out to your bank statement.
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