I am not a CPA or tax professional and you might want to consult one but I have had alot of trouble with Turbo Tax trying to handle 1041's but not my 1040. I did consult a CPA on my 1041 Trust Return issues and he advised to override the program and put in what is supposed to be. Rather than messing around with your staffing agency which might be doing it the wrong way (if they are your real employer and they are the ones issuing you your paychecks under their EIN, they should be reporting it all on one W-2.) I would just insert Schedule 3 into the Turbo Tax program, find the line where you would report the over payments and then click on the little icon to take you to the 1040 Worksheet, right click on line 11, select "override" and just put in the amount you overpaid. Just my opinion but at least then you don't have an issue with reporting to the IRS two EIN numbers that didn't actually report anything. Good luck.
