I am a New York resident and my spouse is not. When I do a New York return in interview mode it does not ask for my spouse's residency. How do I put my spouse is a nonresident? Doesn't this impact the return?
The state return will typically use the same filing status as used on the federal return.
If you are trying to file as married filing separately for your New York return, you will need to set up a mock return per the instructions in the following link. This return will need to be mailed in.