One married couple, two different states

You can file your federal return jointly and file married-separate in each state if you want to. Another option would be to file as married-joint on your federal and state tax returns and apply for a credit for taxes paid to another state. You will see that option on your resident state tax return.

If you choose to file married-joint federal and separate on your state tax returns, you will have to prepare three federal tax returns, one for each state on which you file as married-separate on the federal and state returns, and a third for your joint federal tax return. You would find it helpful to purchase the desktop TurboTax program that you download on your computer if you choose to do this. That way, you can prepare all three returns for the same price.