You are doing it correctly by entering the amount from box 16 of the W-2 for the Wisconsin wages.
TurboTax is asking you the question, as it wants to make sure all the wages and other personal service income (that may not always be listed on a W-2) is entered here.
If it pulled the amount over directly from the W-2 it may miss some income for some people.
Did you do the non-resident (WI) return before the resident return (MN), if not, this may be why it did not carry it over.
