If a want to issue a refund, for overpayments or other existing credits via credit card, follow this procedure.
1: Display the payment that caused the overpayment.
2: Click Refund the amount to the customer in the lower left of the payment screen. Then click Save & Close.
3: On the Issue a Refund screen, enter "Refund of overpayment" in the memo field then change the "Issue this refund via" field to VISA (or other card name).
If you use the QuickBooks Merchant Account service, you should click Process credit card refund when saving before you save the refund transaction. This will process the actual credit to the customer’s credit card.
4: When you refund by credit card, QuickBooks will credit the Undeposited Funds account and tag the transaction with the payment type you selected on the refund. The next time you record a deposit, you’ll see the negative amount in the Payments to Deposit screen. Select this amount along with all the positive amounts for the day and the total “net” deposit will be recorded in your register.
5:If the refund does not offset any other deposits for the day, you will end up processing a negative deposit. QuickBooks handles a negative deposit in the same manner...there is no special procedure to follow.