You can file married joint or separate in each state. You would have to try it both ways to see which is best. Follow the instructions as you work through the program in each state to apportion income. It may be better to use the desktop version of TurboTax rather that the online version since you will only have to purchase one federal program. To file as married-separate in a state, you would have to prepare a separate federal return to complete that state's return. Since California is a community property state, you would have to divide up your income equally for the most part, so it may be easier to file as married-joint there.
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