Assuming your state allows different filing status than federal, you can use the checkbox on the state information worksheet to designate MFS, and use that for the main taxpayer. Then you will need to create a separate file for the spouse, entering him/her as the primary taxpayer, and use that file for state purposes only. I've done that for PA. If that doesn't work for your state, another option would be to create 3 separate files--one for Federal, and 2 for states. Beware that some states don't allow for the filing status to be different from the Federal.