Hello mdj101, thanks for commenting on this thread so you should be able to match the deposit to the banking transaction. in your Quickbooks account. 

You can add to the bank deposit (underpositied funds) and minus the PayPal fees. Put the date of the bank deposit this should match at the bank but you have to make sure the undeposited  amount has the correct bank showing for it to show as a match. When in the banking screen if it doesnt show up as a match then you will need to click into it and click find match and it should bring the deposit up for you to select.