If you are filing Non-Resident returns to the states where you earned income, prepare those first, and your Resident State of Illinois last.
Report only the income earned and taxes paid to that state on your Non-Resident return.
You report all of your income to your Resident State, and get credit for Taxes Paid to Other States, and your Illinois return would show your total income for the year, so it sounds like your Illinois return is correct.
Check your Non-Resident States to be sure that the amount of income you earned in that state is being reported correctly.
Click the link for more detailed info for filing multiple states.
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