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You will only enter your W2's in the federal section. They will then transfer to your state returns based on the states listed on your return for taxes withheld. If you had taxes for both states on both W2's then both of them will be transferred to both states.
If you live in one of the states and work in the other state, then all of the income will be reported on the return of the state that you live in. Only the income earned in the state you did not live in is taxed. Some states start with your federal AGI so it looks like you are being taxed on it, but as you walk through the steps you will see an option to remove the income not earned in the state you did not live in.
Be sure to read and answer all the state questions so you can report and be taxed only the income that should be taxed by that state.
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