Creating Credit Refunds/Invoices
If it's an overpayment, go to Income -> Payments -> Refund Credit.
The overpayment should appear allowing you to refund the money.
If it's a refund, simply go to Income-> Invoices -> New Invoice and create a negative invoice.
To apply this credit toward the existing invoice, enter in a payment of $0 for the customer and apply the negative with the positive.