Please help me on this tax question. grr. ok i am married and my wife and i live in separate states...?

i can understand when filling out tax forms. FEDERALLY combining the income and paying FED taxes on money. but when it comes to filling out STATE taxes. it asks yo to move the combined income from the FED form over. this does not make sense to me because my wife lives in NYC and ALL of her income is from that state. i live in Georgia and only make money in Georgia. but it seems on the state forms i am being expected to pay NYC taxes and Vice Versa?? if we use the combined income instead of ONLY the money made in that state then you are paying taxes in a state you dont even reside.. does this make sense or am i reading this wrong?? .. i mean i dont have NYC taxes taken out of my check but moving the FED money over to state tax forms makes you taxable for a state you dont live in.. can someone please explain this?? her Permanent residence is in NY and mine is in Georgia.