Thank you for your reply.

For clarification, using QB payment link automatically creates a Sales Receipt and Bank Deposit. By creating an additional deposit as you suggested, I'm concerned it would be an duplicate.

For example, I have 5 invoices for $100 each for 1 customer. I send the customer a payment link for $500. QB creates a Sales Receipt for $500 and a Bank Deposit for $500 (along with any other QB credit card transactions for the day). I now have 5 unpaid invoices for $100 each and a paid $500 sales receipt for that customer. 

If I go to the banking transaction that was created for the sales receipt, QB has automatically matched it to the deposit. I can click Find Other Matches, search for the invoices, and select them. The problem is that the additional credit card transactions on the deposit means the deposit is greater than the 5 invoices alone. When using the Find Other Matches and selecting only the 5 invoices from the Payment Link, I receive an error: "The selected and downloaded transaction amounts don’t match. To continue, resolve the difference." The additional transactions do not show up under the Find Other Matches search. 

Any help would be appreciated it. Thank you!