When using the Origin ID Type option as Federal ID, the bank will assign an account prefix before the company identification number in the file. For example 1 = operations account, 2 = payroll account (or a or b) etc.

An enhancement request has been submitted for this scenario.

At the moment, there is not a method through the interface to make the Company/Batch header record reflect anything other than a 1 prior to the federal ID.

You can force a 2 in front of the EIN for the Company/Batch Control Record (Company Identification number) by using the Bank Assigned ID option.

Otherwise at this time, you will need to edit the file in a text editor prior to sending to the bank.

What is the NACHA file format?