Essentially, you need to use a separate “merchant” bank account in QuickFile to represent this. Log payments into this account for the full value of the PayPal sales, log the deposits of the net value in your current account as transfers from the merchant account, and create purchase invoices to represent the fees, paid from the merchant account to balance the books.
http://community.quickfile.co.uk/t/handling-payments-from-merchant-accounts/8865