Allocate PayPal fees to paid invoices (not via R1)

Using R1, I am creating invoices on my website, and receipting only via PayPal. I am entering the full invoice into R1 for each transaction (x). Of course PayPal takes a cut, so I am left with x-fee.
How am I best to account for the shortcoming, or fee on each invoice?

I have reviewed thread at https://community.reckon.com/reckon/topics/fees-on-invoices however this is a Reckon Hosted topic and I'm not sure if it is suitable.

Any help appreciated.