Having three bank accounts with different EINs doesn't necessarily complicate your business tax return - just report the interest income (if any) from each account.
You aren't required to report "bank accounts" on a tax return (except foreign ones), just interest income from the banks.
EINs are there so the bank can report the payment of interest on account balances. If sufficient interest is paid on an account (usually > $10), the bank will send a 1099-INT listing the recipient's EIN. You can report as many 1099-INTs as necessary on your personal (or business) return - as long as the accounts are owned by you (or your business).
