Pipemonk syncs Payment fees by creating a credit note to the payment. The amount in credit note equals to the Payment fees associated with the respective invoice.
(1) This is what an Invoice and Credit note look like:
(2) When you click on Invoice, it will show the respective components of products, taxes and payment (as shown in the below image):
(3) The credit note that includes Payment fees can be seen when you click on Credit Note (See the below image):
This is how Pipemonk calculates payment fees from the Invoice and deposits it in the correct account of expense. Check the pre-requisite conditions to enable Payment Transaction tracking for your Pipemonk account.