Generally, speaking, you pay income tax based on where you are living, or where you actually perform the work, not based on where the company is located. There are a few states that will try to tax you if your employer is based in that state but you work remotely, but Illinois is not one of those states. Therefore, you would only owe Illinois state income tax for any income that you earned or that was paid to you while you were living or working in the state of Illinois. This might include a week of training, or one day a month that you are required to travel to Illinois to attend meetings, and so on. You would allocate your income between Illinois and California based on the percentage of work days that you performed work in Illinois.
If you do have some Illinois work, you would file an Illinois nonresident tax return, and a California resident tax return. You would pay Illinois tax only on the percentage of income earned while you were physically working or living in Illinois. You would pay tax in California on all your worldwide income, but California will give you a credit for Illinois tax that you paid on the same income.
