Option I: Add bank fees through the bank reconciliation:
While in the Bank Reconciliation, Click on the Add Chk/Adj button.
This will bring up an entry screen where you can enter the GL Account number the bank fees will be expensed with a debit entry. The bank account you are reconciling will be credited.
Once you have completed this entry, the item will be in the bank reconciliation under the checks tab, and already marked.
Option II: add bank fees through the General Ledger Individual Transactions:
As you can see, you will want to make this entry a Journal Type: CD If it is not a CD, it will not show up in the Bank Reconciliation.
Also, when you enter the bank fees using a journal entry, you must create both sides of the entry, crediting the checking account and debiting the expense account.