Multiple state tax returns can be tricky. You need to do the Wisconsin return first. If you already did the Illinois return then you should delete it and delete the Wisconsin return you've started and start over by doing Wisconsin first. You should be registered as a part-year resident of Wisconsin and a resident of Illinois. Illinois will give you a deduction for taxes paid to Wisconsin while you were there being an intern but you have to do Wisconsin first to make sure Illinois gives you that deduction.
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