Thanks for the update, afsmith.

You're on the right track in receiving customer payments by creating a credit memo in QuickBooks Online (QBO). Before you can link it to your downloaded deposits, you'll first have to apply it to an invoice. I'll gladly guide you on how to do this below.

Since my colleague recommended turning off the Automatically apply credits feature so the credit won't apply to any open invoices, let's manually apply it to the appropriate one (if you've already created one for them). Here's how:

1. Go to the + New button.
2. Select Receive payment.
3. In the Customer dropdown, select the customer.
4. In the Outstanding Transactions section, select the open invoice you want to apply the credit memo to.
5. In the Credits section, select the credit memos you want to apply.
6. For the open invoice in the Payment column, enter how much of the credit you want to apply.
7. Leave the Payment method, Reference no, Deposit to, and Amount received fields blank.
8. Fill out the rest of the form, including the Payment date. Make sure the total is correct after applying the credit memo.
9. When you're done, select Save and close. 

Once you're done, go to the Banking menu and link or match the invoice to your downloaded deposits in your checking account. For the step-by-step guide, please see this article: Categorize online bank transactions in QuickBooks Online.

Also, I encourage you to reconcile your checking account in QBO regularly (every month) to monitor your income transactions. You may want to check out this article as your reference in doing and fixing reconciliations in QBO: Learn the reconcile workflow in QuickBooks.

Let me know if there's anything else you need in managing payments and customer transactions in QBO. I’m more than happy to help. Wishing you the best!