You can file North Carolina as Married Filing Joint and show that your wife was a part year resident.
Your wife would need to file a Married Filing Separate tax return for Michigan if she has Michigan income.
You can still file jointly for your Federal Return. To file separately for Michigan you will need to create a Federal return for your wife as Married Filing Separate and Part Year Resident for just the state of Michigan.
This is done so that the information can flow from the Federal to the State.
This needs to be done is a separate account if you are using TurboTax online or you can purchase the desktop version of TurboTax and there is no additional cost to create the second Federal Return.
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