You can file your Federal return jointly, even though you live in separate states, and you can list your current addresses in the MY INFO section for each of you.
If either of you moved during the year, you may need to file Part-Year Resident Returns to both states you lived and had income in.
If not, you can each file a Separate Resident State return to the state you lived in all year.
Click the link for detailed instructions on How to File Joint Federal and Separate State Returns.
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