If you file married-joint, you report all of your income in the federal section of TurboTax. It will flow down to the state return. Then, depending on how each state's taxes work, you will see an opportunity to either enter the income earned in that state or you may see an option to get a credit for taxes paid to another state. You will do allocations as required based on the income applicable to each state, not according to who earned the income.
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