You can add a negative line item to Invoices to denote PayPal fees. For example, if you invoiced someone for $100 and only got $95 from PayPal and applied it to that invoice, it'd look like $5 was still owed. To reconcile this, add an additional line item titled "PayPal Fees" (or whatever you'd like) with the amount of -$5.00. This will deduct $5 from the total ($100) so that the payment of $95 will balance the invoice and mark it as paid in full.