Lee kivi,
Welcome to the club web site...
I've fished the Winnebago system many times, for walleye, perch,gills, white bass etc. but never really targeted Muskies , rommor has it that there are some trophy class Muskies swimming in them waters..
You asked where can you find them..
thats a hard question to answer as you have to look at the big picture the winnebago system consists of a number of lakes connected together, lake winnebago is the largest 137,708 acres with 88 miles of shore line with an avereage depth 15.5' and a maximum depth of 21' then you have Lake Butte des morts, lake winneconne,lake poygan, plus the fox and wolf rivers some 166,800 acres combined.. the old saying muskies are a fish of a thousand casts definatly apply here LOL I know that the Wisconsin DNRs stocking program includes stocking muskies in the winnebago system most of which, if not all have been stocked in the upper lakes (poygan and winneconne) I personaly would start there and work my way down to winnebago ,working the weed beds,downed timber, rocky shorelines.. and the canebeds on lake butte des morts for starter.. baits: bulldawgs,depth raiders,suicks,ducktail weed warrior jerkbaits.
Again welcome to the web site ..
just to let you know each year a group of us member here on the BB get together to fish the Mississippi river by La Crosse Wisconsin if your interested in joining us for a great time Check out My La Crosse get together post under the meets topic ..
Take care and good luck fishin 
"Friends are GOD's way of showing us that we don't have to fish alone"
"Take a child fishing"
(Wi) Life Member
Jerry K.