If you receive a payment, and the amount is higher than the outstanding total, the system will automatically retain the difference, and use it as a credit on future invoices. When applying the payment, you will see an "Overpayment" notice with the total amount of the overpayment.
How to create an prepayment credit
Applying a Overpayment to an Invoice
If a customer has credits due to overpayments, they will be automatically displayed for the selected customer as Open Credits.
Notice that the notes you add to a payment are also available for credits (overpayments). Once you hover the mouse over the note icon for a prepayment, the added note will be displayed. If you select several credits that have notes, they will appear separated by a semicolon. These notes could be useful to indicate which invoices a credit should be applied to. Click on the image to see the details.