Let me help you from here, Sarah17.

When a customer overpays, it will create a credit on their account. Then, you have three options on how you can handle the overpayment:

• Apply the credit to an old invoice or future invoices
• Refund the customer
• Record the overpayment as a tip

In your case, you've sent a refund check to your customer. It means that you'll also have to create it in QuickBooks Online. This way, the matching of downloaded and existing transactions will be easy. I'd suggest deleting and starting over to ensure that we'll record it correctly. Next, record the payment the usual way so it will create a credit. Then, create a customer refund. 

You can also check this article for better guidance: Handle a customer credit or overpayment in QuickBooks Online.

If any questions arise, please feel free to leave a comment below. We'll get back to you as soon as we can.