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Illionois and Indiana do not have a recipricol income tax agreement. This means that your employer should be taxing you based on your illinois sourced income for illinois.
This also means that you will have ot file two state returns.
1. You will file an illinois non-resident return and claim any refund due to you by illinois.
2. You will file an Indiana resident return. Because you are a resident of Indiana, Indiana will tax your world wide income. However, you will get credit for paying taxes in Illlinois. If the Indiana tax is greater, you will have to pay the difference.
NOTE: these states have recipricol agreements, just not with each other.