My employer had my home address as a WI address for the first few months of 2016 when I live and work in MN for all of 2016. Taxes were paid to WI. How do I file this?

Yes, because you paid WI state income taxes, you will need to file a State Income Tax Return for both Wisconsin and Minnesota. Since your tax home is MN, you should prepare your nonresident state (WI) return before you start your resident (MN) return. Be sure to indicate that you earned income in more than one state (see attached screenshot).

See this link for more information: How do I File a Non-Resident State Return?

Wisconsin and Minnesota have a "reciprocal" agreement with regard to income taxation. In other words, you only pay taxes in your home state. TurboTax will handle this for you. Be sure you answer all questions as accurately as possible to ensure the best possible outcome in your situation.