I can show you the easy steps on how to link the customer's credit to their open invoices. If you used a journal entry, be sure that the affected credit account is Accounts receivable (A/R) and named to the customer.
If you haven't yet created a journal credit or credit memo, here's how:
Journal Entry
Click +New and select Journal entry.
Enter the journal date.
On the first line, select the Debit account and amount.
Then on the second line, the Credit amount and Accounts Receivable (A/R) account. Under the NAME field of the second line, select the customer's name.
Check if the amounts are balances and then Save and close.
Credit memo
From the +New button, click Creditmemo.
Select the customer's name and the credit details.
Enter the item and amounts.
Click Saveandclose.
After you've decided how you wish to enter the credit, you can use the Receive payment option to link the credit to an open invoice.
Click +New and then Receive payment.
Select the customer's name.
Check the Invoice and then the credit you created under the Credit section.
Review the amounts and then click Save and close.
Feel free to use these links in handling customer payments: