A tax filing question?

I am filing married this year-should I file jointly or separately since my spouse is in the military and I was in college and we lived apart the entire year? Also, so far on turbo tax it is telling me I get no state refunds and a very low federal--is this correct and is it because I am now married whereas before I always got a higher federal refund and state refunds?? How come it will not let me enter in educational deductions just because I am married filing seperately?