This article is about entering BNB third currency fees manually, the API imports them automatically, the CSV has the option to generate them with this button:
Currently the BNB you use for a trade fee in Binance can not be deducted automatically from the Balance, if BNB is not one of the exchanged coins.
Basically the fee field is only for information purposes and the trading fee pages. No calculations are done with it that affect the balance of a coin.
This is why the fee needs to be part of one of the fields that affect balance and purchase pool (buy or sell).
In case of a sell, the fee needs to be entered as additional amount on the sell side.
In case of a buy, the fee needs to be subtracted from the buy side.
You could say you enter the "actual received/spent amounts", with fees included.
BNB is a special case since it represents a third currency (i.e. a coin that is not part of either the sell or the buy) can therefor not be deducted from the total balance by being included in the sell or buy sums.
In order to correct your third currency coin balance in the portfolio, you need to create an additional transaction as "Other Fee" for the fee on the Enter Coins page.
This will be done automatically with the API and CSV importers.
