Thank you for providing details of your concern, @jkope26!

Let me help you match your invoices in QuickBooks Online.

When recording a payment via bank deposit, it will not be applied directly to the open invoice. You'll have to enter the customers' payment via the Receive Payment screen and match it with the deposit.

You can exclude it and create the deposits manually.

Here's how: 

1. Select + New.
2. Click Bank Deposit.
3. From the Account ▼ dropdown, choose the account you want to put the money into.
4. Select the checkbox for each transaction you want to combine.
5. Make sure the total of the selected transactions matches your deposit slip. Use your deposit slip as a reference.
6. Click Save and new.

Make sure everything matches between invoice and payment, like dates, etc.

You can check this article: Matching transactions. You'll avoid getting duplicate records of your transaction in the bank register.

If there's anything else that I can help you with, let me know in the comments. I'll be here to lend a hand.