Write a cheque to the customer. In the account, use 'Accounts Receivable'. Tab over to the 'Customer:Job' field, and type in your customer's name. Now this cheque has just offset the credit that you have previously applied to their account in the A/R module. The second step would be to go to Receive Payments. Type in the customer's name. Apply the outstanding credit against the cheque amount that you just paid, which will be showing in the window.