TurboTax will ask you questions as you prepare your tax returns but it will not tell you how to file your tax return as far as filing status. Is there a reason you filed separately in Iowa? Did you work there and were the only one with income sourced to Iowa?
Depending upon your situation, Iowa typically is filed using the same status used on your federal return. However, if only one of you has income from Iowa, then you could file separately.
Please see the link below for more information on the filing status that you could have used to prepare your tax return.
Iowa filing status
Form IA 126 would have been prepared if you have prepared your tax return to reflect both your resident state and your nonresident state information when you completed your return. If it was not included, you should consider amending your Iowa return to correct the state return and report everything accurately.
IA Form 126 and instructions
Please see the link below for additional guidance on how to amend your state return.
Steps to amend a state tax return
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