To apply a payment received from a customer, click Apply Payment from the left sidebar in the main window, or click Payment from the main toolbar. In the Payment window, enter the date the payment was received, then select a customer or invoice number to bring up the amount that is owed. If the payment received does not match the amount owed, you can change the amount, and the customer's account balance will be updated. Select the method of payment, and enter a reference number for your records (optional). Click Record to record and to apply the payment to the customer's account balance.

Note: Express Invoice uses an account-based payment system where payments are applied to the customer's account - not to a specific invoice. This makes it able to handle advance payments or payments without specified invoice numbers much better. When you receive a payment, the payment is applied to a customer not a specific invoice. You can, however, enter a soft cross-reference between a payment and invoice. This is for reference and ease of use only and is optional.