If a customer has partially paid for the items sold then it easiest to follow these two steps:
1. Create a Credit Memo for the unpaid balance of billing- The process to create a credit memo is almost the same as creating a manual billing. The main difference is that when the billing lines are entered, they are entered with negative values. This will automatically change the invoice to a credit memo. The transactions created when posting a credit memo are a debit to the GL Revenue Account selected on the billing line, and a credit to the AR Control Account. 
Tip - To associate the credit memo with an original billing, place "Credit Memo for Billing number xxxxxxxxxx" in the Proprietary Billing Number field.
2. Apply the credit memo to the billing. See the video above.
3. Create an Account Payable to the customer for the amount originally paid and to be refunded. The amount to refund on the account payable line should be positive. The value for the product on the Account Payable line should be blank or null.
Tip - In the Payee Reference field of the Accounts Payable, indicate the Billing and reason for the refund to the customer. This explanation will be printed on the check or if a credit card transaction can be useful in reconciling the account.
4. Create a Cash Disbursement by following the standard instructions for creating a single or batch cash disbursement(s).


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