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Husband lives in California, and CA withheld CA tax, and wife lives in Virginia, and Va withheld Va tax
this may depend on your tax software you are using. are you using the one built into canopy or a seperate one?
we use Drake. in Drake i can indicate that the other spouse is a nonresident of the state and set the appropriate individual as the resident and file the federal with two states (or more in some cases).
hope this helps
You can also usually file MFS for each state as well. Then as Brielle said, name the resident and show the other as non res. Each return stands on its own. You can still file MFJ for Federal and separate for state.