Q. So this mean that TT will make our Federal filing "Married jointly", but State filing will be separate as one state each?
A. Not necessarily. I'm not specifically familiar with PA and SD rules and software. But, it is common to be able to file a joint state return, with one spouse being a resident and the other being a non-resident. You would only pay tax on the income of the resident spouse. Some state allow you to choose between filing separately or jointly. If that's the case, in PA and/or SD, the TT software will handle it.
It's not clear why you are trying to do this. Even as a SD resident, you would have to pay PA tax on your PA wages and then claim a credit on the SD return.
