The Credit button at the top of a customer's profile will add credit to a customer's account without payment.
If someone makes a payment for more than one month at a time use the prepayment option under Make a Payment.
When using the prepay option use the custom option under the prepaid plan drop-down. The monthly price before discount is the price the customer pays per month (not the total amount of the payment). The billing cycle is the number of months the customer has paid for. Double check the 'Prepayment Summary' to be sure it shows the correct amount as well as the right date in which the customer has paid to. Choose the payment type and hit the make a payment button at the bottom of the screen.
If your customer account shows outstanding and credit but a zero balance, use the Make a Payment tab, then click the blue pay to the right of the line item.
This will bring up a screen that allows you to mark the line item as paid with credit.