Hotels in Wisconsin you can book at 18
When a front desk enforces a minimum age of 21, an 18-year-old holding a reservation still gets turned away. Both of the Wisconsin cities covered here have hotels that welcome 18-year-old guests. Start with whichever city your ticket or arrival plan points you toward.
21 hotels
Madison
10 hotels
Milwaukee
Your base is set by train station or Thruway motorcoach
Wisconsin's passenger rail station list includes Milwaukee Intermodal Station and Milwaukee Airport Rail Station, and Madison does not appear on that list. WisDOT lists Madison instead under Amtrak Thruway motorcoach connections, which are bus legs rather than passenger rail stations. For this comparison, that makes Milwaukee the covered passenger-rail-station endpoint and Madison a Thruway motorcoach, or connecting-bus, endpoint.
Your arrival mode therefore does some of the choosing for you. If the last leg of your trip ends at a passenger rail station, Milwaukee is the covered city that has them, so read the Milwaukee hotels first. If your Amtrak itinerary finishes on a Thruway motorcoach into Madison, the Madison list is your list. Neither of those facts promises a departure, a fare, or a seat on your date, so confirm the leg itself before you book.