Hi satureyes, thanks for dropping by on this thread. You can record third party transaction fees by selecting the 'undeposited funds' under the 'deposit to' account on the invoice, and then follow the steps below to record the deposit:

1) Select + New > Bank deposit

2) Select the date that the payment was received and tick the invoice under 'select the funds included in this deposit' 

3) Scroll to 'Add funds to this deposit' and select the fee expense account under 'Account' and enter the total fee amount as a minus figure with no VAT

4) Save and match to the bank transaction