You figure the percentage applicable to Wisconsin, and that much is not taxed by Wisconsin. The remainder of the tax exempt income is taxed by WI (not by the IRS).
So, what you must do is "add back" the total tax exempt amount minus the not taxed by Wisconsin. You do that during the state tax return interview questions. There is a section for Additions to the federal adjusted gross income (AGI) and you put the amount taxed by WI in that section or in response to a question in that section.
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