Is this service going to be a branch of the existing CN route that the Empire Builder uses? Are they planning to run through trains to the Twin Cities or just terminate in Madison? Looking at open Railway Maps, it seems that there's a branch line that turns off the Empire Builder route at Watertown, approaches Madison form the northeast, runs through the Isthmus, and then heads west croiss country along the Wisconsin River to Prairie du Chien and the tracks along the Mississippi, where it can turn north and rejoin the Empire Builder route at La Crosse.
No trains would run just MSP-Madison. There are to be CHI-MKE-MSN trains which terminate in Madison, while others run CHI-MKE-MSN-MSP via Eau Claire or (potentially) La Crosse.
Westbound the trains will follow the CP tracks from Chicago to Watertown (same as the Empire Builder) where they will branch off toward Madison on the Wisconsin and Southern line. Then heading out of Madison they would run north on CP tracks and rejoin the Empire Builder's route just east of Portage. Heading northwest prior to Tomah it will branch off at Camp Douglas onto the UP track through Eau Claire toward MSP. It's also possible as some point a CHI-MKE-MSN-MSP train could stay with the CP tracks and follow the Empire Builder routing through La Crosse and northward into MSP, but MSN-MSP via Eau Claire is the near-term plan.
The Empire Builder and the second TCMC starting soon between St Paul and Chicago will both rollow the CP route and bypass Madison with a Columbus stop.
From the WI state rail map 2023 https://wisconsindot.gov/Documents/travel/rail/railmap.pdf