Go to A/R>>Receive Payment.

 Use the available filters to find the customer.

 A link will inform the amount of money that the customer currently has in open credits.

Click on the link "Click here". The system will open the Available Credits window. There you will visualize all the credit types the customer might have: Prepayments and Customer Credits. Select Customer Credits and click on Close. 

In case you are going to receive an additional payment by the customer, enter the its amount.

Select the payment Date , method, and reference #. 

Click on Apply for the specific order you want to pay (Notice that there is a button called Auto Apply Payment which will automatically apply the payment amount entered starting with the oldest invoices).

Click Save & Print, Save & New or Save & Close to finish.