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 a payment on the Invoicing Screen. If you use the second method, you will need to issue a statement, or the client won't see the credit. Also see the FAQ topic How do I apply a percentage discount to an invoice?