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If you have several homes - you primary residence - is the place where you live most of the time.
You and your spouse do not have to have the same primary residence - you may live separately based on your specific circumstances.
Either if you live together or separately - you generally have a choice - to file a joint tax return of to file separate tax returns.
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For federal tax purposes - you may file either a joint tax return or separate returns.
In most situations a joint tax return provides better refund, but you would need to make all calculations and compare based on your specific circumstances. Most tax preparation software allow to compare MFJ vs MFS options.
For state tax purposes - each state has a separate requirements and income tax laws - that should be very specific for your situation, Most states require to use the same status as on the federal tax return.
The issue may be if you sell one or both of your homes. You may be able to exclude the gain from your primary home. The gain resulted by the sale of a secondary home is taxable.
Let me kno wif you need any help.