You should be sure to select the proper Home Of Record (or state of residence) for each of you in the "My Info" section. (you both may claim the military Home Of Record). If your spouse is stationed anywhere other than his Home Of record, you file as if he is living there.
You would file the same way as if your spouse was not in the military (MFJ or MFS).
There are some other exceptions to tax treatment compared to non-military, if you have a specific question, please post an additional question.
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