The best alternative for you will be to file jointly on your Federal tax return, and separately for the states. This can be a little tricky. It would benefit you to get the Desktop CD version.
- Prepare one married filing jointly (MFJ) return to file with the IRS.
- Prepare a mock married filing separate (MFS) return for each taxpayer.
- Then for the first taxpayer, label and use the first mock MFS federal return to prepare their state MFS return.
Also see: A married couple living in different states
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