There are two ways to do this. You can add a negative fixed-price entry in the Time & Sales screen. The entry will appear on the next invoice and deduct itself from the total of fixed hours. The other method would be to receive apayment on the Invoicing Screen. If you use the second method, you will need to issue a statement, or the client won't see thecredit. Also see the FAQ topic how do I apply a percentage discount to an invoice?