Thanks for sharing detailed information about your concern, @LMcm4Rays. Let me add some insights to properly record the double payment of your customer.

When a customer overpays and you receive the invoice payment, QuickBooks saves the excess amount as available credits on their account. If a customer doesn’t have existing credits on their account, here’s how to create a credit memo.

1. Go to Customers, then select Create Credit Memos/Refunds.
2. Enter the items you're giving credit for, then select Save.

Then, you can either write a refund check or apply the credit to an invoice. Let me show you how.

Write a refund check

1. Go to Customers, then select Create Credit Memos/Refunds.
2. Select the credit memo you'd like to create a refund for.
3. Select Refund. This opens the Write Checks window.
4. This creates your check and auto-populates the details. Review and select Save.

Apply credits to an invoice

1. Go to Customers, then select Receive Payments.
2. Select the customer on the Customer: Job ▼ dropdown.
3. Select the Apply Existing Credits? checkbox.
4. Hit Save.

I'm also adding this article for more details about creating customer refunds: Record a credit memo or refund in QuickBooks Desktop for Mac.

Let me also add this article that can guide you in adding and reconciling your accounts effectively in your QBDT software: 

• Add and match Bank Feed transaction
• Reconcile an account in QuickBooks Desktop

Keep in touch if you need any more assistance with this, or there's something else I can do for you. I've got your back. Have a good day.