1. Select Tasks > Receive Money.
2. Select the Customer ID.
3. On the Apply to Invoices tab, select Pay box next to the credit memo you created.
4. Select the Pay box next to the invoice you want to apply against the credit memo.
5. Enter the rest of the required information (Reference, Date, and so forth), and then click Save.

 TIP: If you want a zero receipt, you can change the amount paid on the invoice if the total invoice is a different amount. 

How do I enter a customer credit memo against an invoice without returning items into inventory?

How to Enter a Customer Credit Memo