For the open invoice in the Payment column, enter how much of the credit you want to apply. You have to tell your credit or debit card company about any error you're disputing within 60 days of when the first statement with the charge was sent to you.Here are instructions to receive a customer overpayment then issue a check refund for the resulting credit balance using QuickBooks Desktop. In SumUp Invoices, go to the 'Credit Notes' tab and click 'New Credit Note'. To help you properly handle an overpayment from a customer in QuickBooks Desktop Enterprise, you could follow these steps: Option 1: Create a Credit Memo.