The first question is where is your wife's domicile? Domicile is a tax concept something like permanent residence, it is where the majority of her financial, family, social, legal, and other ties are. Where her doctor, dentist, voter registration, significant friends, church membership, and so on are located. No single factor is controlling, it depends on the balance of all factors. A taxpayer can only have one domicile at a time, no matter how many homes they have.
If her domicile is still with you in state A, and I think this is the most reasonable answer for your circumstances, then you file the following.
a) federal married filing jointly
b) a state B non-resident return. She must report income earned while living in state B only, and pay tax on it. This can be a joint return since you don't have income in state B.
c) a state A resident joint return. She reports all her world-wide income, including state B income, and you report all your income. You pay income tax to state A, but you get a credit in state A for taxes that she paid in state B, which limits double taxation.
If you want to argue that she has changed her domicile to state B, then you need to file state A as married filing separately and she files state B as as married filing separately, to avoid you both being taxed in both states. This gets complicated, especially if you want to file a joint federal return -- which you probably should do since married filing separately has higher tax rates and many deductions and credits are reduced or disallowed. We can give you more details on how to do that if you think that applies to you.
