Under the firearm in a vehicle transportation statute (167.31) the law says all long guns must be unloaded, but handguns may be loaded. The definition of unloaded is no shell in the chamber nor magazine, and any loaded detachable magazine or feeding device cannot be inserted into the firearm. Guns no longer must be encased while inside a vehicle. Ammo does not have to be totally separated from a firearm, a detachable magazine may be loaded, as long as it's not "in" the firearm.
But here's were the "handguns may be loaded" gets ambiguous... under the concealed weapon statute (941.23), any firearm in a passenger compartment that is within reach of any occupant, and is "below the window-line", is considered a concealed weapon, loaded or not, encased or not, handgun or long gun. I'm not aware of anyone who has been cited for an unloaded and encased handgun, or long gun, sitting on a seat... but it IS illegal. However, if a loaded handgun is within view from outside the vehicle at a short distance, such as on the dashboard, that is technically legal open carry.
WI honors MO permits that were issued after 8/28/13 only. WI also honors non-resident permits issued by any of the states whose permits are honored (in fact, for VA, ONLY non-res permits are honored). The 2 most "popular" non-res permits out there are UT & FL. WI does honor UT, both resident or non-resident (except for a WI resident with a UT permit), but does not honor any FL permits.