I just tested with online TurboTax and even in online TurboTax I do not get the Yes/No question if the Forms W-2 have different EINs. But as with the CD/download version, if the EINs ar the same, TurboTax ignores the answer to the Yes/No question and treats the Forms W-2 as being from the same employer.
If the employers are different, they must have different EINs. The payroll service should be putting each separate business's EIN on the Forms W-2, not the payroll service's EIN. If the payroll service is putting the same EIN on both Forms W-2, they are saying that both Forms W-2 are from the same employer.
https://www.irs.gov/government-entities/third-party-payer-arrangements-payroll-service-providers-and...
