It depends. If you have a residence in Virginia and were present for at least 183 days in Virginia, Virginia considers you a statutory resident. However, you are a domiciliary resident of South Carolina because that is where your main home is. This means that you are going to file a South Carolina resident return, Married Filing Joint, regardless of how you file the Virginia return. For Virginia, you will file one of two ways:
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Resided in VA less than 183 days, or do not maintain a residence there. You are a nonresident. You will file a nonresident return. Only your income in Virginia is taxed, and South Carolina will give a credit to your income tax you pay to VA on this income.
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Statutory VA resident. You would file a Virginia resident return, but Married Filing Separate. Again, the tax you pay on your income in Virginia is a credit on your South Carolina return. To file a joint Federal and a Separate State Return, please see this FAQ on how to do this: https://ttlc.intuit.com/replies/3301995
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