How to Apply a Credit Memo to an Invoice in QBO
Go into Receive Payment on an Invoice. It will auto populate, but ignore that. Under Amount Received at the top of the payment window, enter $0. Then mark the box to the left of the invoice, it will populate with the full amount of the invoice. At this point at the very bottom you will see "Amount to Credit" is a negative amount. Now mark the box to the left of the Credit Memo. It will auto populate with the open balance of the CM, which should match the payment amount you put in on the line above. Now at the very bottom it should say Amount to Apply, which should equal your CM and then Amount to Credit will be zero. Save and close.
How to Create a Credit Memo in QBO
Under the Customer, click the green "New Transaction" button. Choose Credit Memo from the dropdown. Fill in the appropriate information and click "send" to email to the customer. Add appropriate verbiage to the email body before sending.
Refunds
Refunds for electronic checks and credit cards can be made from the Quickbooks Payment center. As of April, 2024 QB says it's not possible to issue refunds for ACH payments. If this becomes availalble, it will probaly be visible by opening the specific payment and clicking on the bottom under "more>refund".
To enter a refund made manually with a paper check sent to the customer:
Go the the checking account. Add the customer as the payee. Use account "Accounts Receivable." It is very important to use this account! Enter the amount and save. You should see the credit zeroed out in the customer's account.