Banking

I appreciate you for sharing a complete details about your concern, @hones720.

When record customer refund in QuickBooks, you'd want to make sure to select the same method the customer used in paying you and bank account where the actual payment was posted. This way, it make sure that your bank balance is correct. Also, this makes matching your transactions a lot more easier. I've added a screenshot for your reference.

1. Go to the + New icon.
2. Select Refund receipt.
3. Choose the name of the customer you want to refund from the Customer ▼ dropdown.
4. Fill out the fields using the info from the original sale.
5. Pick Credit Card from the Payment method drop-down.
6. Make sure to select the same Bank account you wish to refund the customer from.  
7. Click Save and close.

Once completed, you can now match the manually added transactions to the downloaded ones. 

You can read through these articles to help you manage your customer-related transactions:

• Void or refund customer payments in QuickBooks Online

• Categorize and match online bank transactions in QuickBooks Online

Keep me posted if you have other questions or concerns by leaving your comments below. I'm just a few clicks away.