How to reconcile paypal bank feed when only net amount is imported?

How to reconcile paypal bank feed when only net amount is imported?

Hello, I can't figure out how to reconcile my Paypal bank account, as only the "net" amount is imported. For clarity:

The sale occurs via my website, which is not connected to Books.
I create an invoice manually. (I'll use $500 for example.)
I have set up Paypal as a bank account in Books.
The bank data feed works correctly. 
The downloaded transactions are $17 for the Paypal fee, and $483 as a "net" amount.
(If the gross amount were download, I would match the $500 payment to the invoice, and create a separate expense for the $17 fee.)

I don't understand what the correct process is to record a payment to the invoice when the net amount is different than the invoice amount. 

I also don't understand how to reconcile my Paypal bank account when the transaction amount shown ($483) is different than the invoice amount ($500).

Thank you for your help.