Let me ease your confusion, Kay03.

Base on your situation, Jen_D's steps are a better option for you. I know the steps let you create a deposit. No worries, though. It won't lead to duplicate transactions. You'll have to match the downloaded transaction to the existing deposit in QuickBooks Online to avoid any duplicates. 

To record the payment properly, you'll have to receive the invoice payments, deposit them to the Undeposited Funds, and deduct the fee from there. Then, you can match the downloaded deposit to the invoice payment.
 

You can follow Jen_D's steps above to help you. 

If you have more questions, please feel free to get back to this thread. We'll answer you as soon as we can. Keep safe!