Reciprocity agreements mean that two states allow its residents to only pay tax on where they live—instead of where they work.  You should have filled out a  Form W-220 and submitted it to your employer.  You won't have to pay Illinois tax as a result of the reciiprocity agreement, but you will have to file a non-resident Illinois tax return in order to receive a refund of the Illinois tax withheld.  That is in addition to your Wisconsin resident tax return.  In the Illinois non-resident return, you will indicate that none of your income is taxable by Illinois, and you will receive a refund of all the tax withheld.

@DavidD66 I really appreciate your help. I've worked for this company for years and this just happened. in the past I always paid wisconsin taxes. so do I need to file my taxes as is and pay the wiscosnin tax and then after I file everything file out the other form to get my illinois refund?

@fwhassler1 Actually, since you work in Illinois, the form you must submit to your employer is Illinois Form IL-W-5-NR, which you can download here:  

https://www2.illinois.gov/rev/forms/withholding/Documents/currentyear/il-w-5-nr.pdf

You must submit a non-resident tax return to IL, allocating zero income to IL, in order to receive a refund of the incorrectly withheld IL taxes.

And you must submit a resident tax return to your home state of WI.  All your income is taxable by WI.