Generally, if you and your spouse are filing a joint federal return but you work in or are residents of different states, you need to file separate state returns. Sometimes this is required by state tax law; other times it is to your best interest to not include your non-resident spouse's income on your state return.
If you file jointly, you cannot list the two different addresses on your federal return but this is not a critical issue for your federal return. Just pick the address you wish to be printed on your joint federal return. This is a critical issue in your state returns and these would need to be filed separately. Please refer to this Turbo Tax link for more details.
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