For states with reciprocity agreements, you only pay taxes in the state where you live, not the state where you perform the work.
If your employer has withheld taxes for the work state instead of the resident state, you'll have to file a non-resident return for a refund from your work state. You'll still file your resident return that also includes that income and pay tax on it.
TurboTax handles reciprocal states and will generate the correct state(s) based on your personal information and your W-2.
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