I appreciate the complete details you've provided, @ss2235.
When you receive a deposit from your QuickBooks Payments account, you’ll need to record the deposit and fees in QuickBooks Desktop. This is so your deposits in QuickBooks match your bank account. Also, the amount you received from the invoice will not match your bank statement because of the fees. You'll need to record the fees correctly so when you create a merchant service deposit on your QuickBooks Desktop (QBDT) it will match on your bank statement.
You can check out this article for more information and for the steps on how to manually record your deposits: How to record merchant service deposits.
On the other hand, here is the correct workflow to record your Account's receivables in QuickBooks Desktop.
- Create an invoice
- Record a payment
- Deposit customer payments
To help you check review the account's where your payments where recorded or deposited, you can pull up Transactions List by Customer report. You can filter this report to show payments you've receive per customer and where it was deposited. Please refer to the screenshot below:
Feel free to let me know if you have other questions about recording your payments. I'm always here to help.