Hi mdj101, 

Although your thread was posted quite sometime back, this Paypal Fee issue is still unresolved. The QBO customer service team did not offer any valid help.

QBO extract the gross amount for Paypal.

Steps worked for me:

1. Banking tab -> Paypal -> Match the gross amount with the invoice

2. Extract transaction fee from Paypal Statement -> book them via journal entries.

Hope this helps!

Lil