When you receive a payment from PayPal, you should in effect have 3 transactions for every 1.
In this screenshot, I have the 3 transactions for a Stripe payment, but the concept is the same.
+£5.00 - This would be tagged to the invoice
-£0.32 - This would be your fee, tagged to a purchase for Stripe in my case (PayPal in yours)
-£4.68 - This is a transfer to the main bank account which is what I actually see of the money the client paid.
I’m not 100% sure, but the PayPal feed may already import the fees, which in that case just tag to a purchase for PayPal (or you can tag straight to Bank Charges, but I prefer setting up a new purchase)
Hope this helps 