Use the Bank Reconciliation screen from the Tasks menu. In that screen you can choose the accounts to be used for posting the charges, and interest, and enter the amounts of each.
If the amount for check printing charged by your bank is automatically drafted from your account balance, then I'd recommend that you enter it as a service charge when doing the bank reconciliation.
To add a new reconciliation, you simply start from the activity showing on the screen for the bank account selected. When you do your actual bank reconciliation, you'll enter these fees along with clearing the items on your bank statement. Once you have the statement reconciled, then click OK. Any fees entered in the Service Charge field, will credit your bank account selected, and debit that account you chose.
Return to Bank Balances, Accounts & Reconciling