You have to file where you make money. For active duty, your military pay always applies to your home of record. You'll see the tax deductions for that state on all of your LES's. If your spouse works, s/he has to file in the state you live and maybe the state s/he works (depends on whether or not the states have a reciprocal agreement).
Ex: My wife is active with home of record WI. We have a rental property in MS. We live in CA (own home) and I don't work. We file in WI and MS, but not CA because none of our income has anything to do with CA. (Made the mistake of trying to file a $0 CA return the first year we lived there. Waste of money.)
Ex2: We live in MS, but don't have a rental property. I work in LA. We had to file in WI, MS, and LA because LA and MS don't have an agreement, so I had to report my income to the state we lived in and the state I worked in.
Sounds bad, but turbo tax sorts everything for you pretty easily.
