LT, being from WI, I usually launch in LaCrosse at the Municipal Launch in downtown. Very nice launch and parking area. Once launched, you are on the Black River which is a slow no wake area. That lasts a few miles until after the train bridge. Then there is a short ride until you are out on the Missi.
Area North of LaCrosse is the best for scenery, river towns etc. If you have a radio, tune to channel 14 and monitor the locks as barges have the right-a-way and can take up to 2 hours to lock through.
As Troutly said, many good places to eat and stay along the river. Stay within the markers and your clear. Your boat will stand out for the water patrol both in Red Wing and the St Croix so be careful.