Hello,
My wife and I bought a home in Indiana. My job forced me to move to the Maryland DC area. Now since I own a home and file jointly with my wife in Indiana they want us to pay state taxes based on adjusted income which includes mine. I pay state taxes to Indiana and not to Maryland. Am I in the wrong for paying Indiana and not Maryland? Or will I be taxed twice as Indiana wants me to pay them from what little I understand of their tax laws. Basically my question is what makes you a resident and does having your better half living in another state put you in double jeopardy? I think I need to anti up a years worth of taxes for MD and deal with Indiana.

Sounds like you are a resident of MD and your wide is a resident of IN. In this case you pay MD taxes on your income and IN taxes on your wife's income. You should have your employer change your withholding to MD from IN. I assume in all this that you are indeed spendig more nights living in MD than IN.