I have a fair amount of experience on more upstream sections (Sauk City down to Spring Green)…
The Wisconsin River is a great fishery. Lots of smallmouth and a fair amount of walleyes/saugers. Lots of “other” fish too (Sturgeon, cats, muskie, panfish, rough fish…). Much of the river is shallow and swift and generally doesn’t hold fish. Best spots to try will be in or near deeper water (3+ feet) with moderate current. Look to the downstream side of breaks in the current (sand bars and points) and any type of structure like rocks or trees in the water.
I have decent success with cranks, plastics, and crawlers. I try to stay away from live bait if I can though. Lots of rough fish around.
Two specific things to try… Casting cranks to the downstream side of sandbars and trolling cranks upstream in the deeper water often produces eyes. Rock shore lines and trees often hold smallies. Any fishy looking spot should be investigated though, odds are good it’s holding something.
The depth of the river changes frequently and fast, with many parts being very shallow. Be aware that the river is not well channelized or marked in anyway and can be very difficult to navigate with a deep boat. The water should still be up this weekend which may be very helpful.
There are also some special regs on the river. Walleye are 18″ minimum and Sauger are 15″ minimum with a combined limit of three in total. Glass bottles and fireworks also strictly prohibited.
There are also a fair amount of back water areas on the river that usually hold good panfish and largemouth.
Finally, bring plenty of terminal tackle. The river is very snaggy.