Payouts arrive with the fees already gone
eBay, Etsy and Amazon deposit what is left after their fees, so the bank only ever sees the net payout. The simple way is to record that payout as Product Sales and stop there: your profit is still right, because the fee never reached you. You just do not see the fee as its own line.
If you want to see fees, import the marketplace's own transactions or payout report as a CSV into an account named after the marketplace, so each sale, fee and shipping label is its own row with its own category. Then open the matching payout in your bank account and switch on Exclude from reports, so the same money is not counted twice.