I am using Quicken Home Business Rental property

This is the scenario, I use Paypal for my credit cards when taking them from a customer.
I am not on-line anything, no banking etc. on Quicken. When I take a payment from a customer it is the total amount of the invoice, then paypal charges me a fee when it is moved to my bank (through Paypal). This is my problem, when I reconcile my check book the bank only gets the amount less the paypal charge, but the full total of the invoice is showing under Deposits in my Reconciliation page. I have set up a Paypal account and enter the charges there and they show up on the Payments and checks side of the Reconciliation page. But with the full amount showing it going into the bank, I can't reconcile my account. How do I handle this?

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