Using the procedure described here, customers who have a negative balance (this means they owe the store money / have been making purchases on their account) can make a payment on their store account. You can also use this procedure to add a positive balance to a customer account (store credit - where the store will owe them money - typically as a result of a return that you did not give cash back on).

1.  At the POS, start a transaction and select a customer 

2.  In the Customers Lookup Form, select the customer 

3.  Click on View/Edit Selected

4.  In the Customer Form, click on Make Payment.