Okay, but did you make those payments using the business EIN (and the correct one?) or your SSN? Also, your statement of "to the comptrollers office" does not sound like a payment of federal taxes to me. Sounds more like a payment of state taxes, county/city/town taxes or something like that. If so, those payment have nothing to do with your federal taxes. Federal quarterly payments are made to the IRS - not any "comptroller's office".
