There is one boat that goes from MK to Wilderness Lodge to Fort Wilderness. Another runs between the Contemporary, Wilderness Lodge and Fort Wilderness. They start running at about 8:30 and continue until after MK closes.
There is a boat that runs from the Contemporary to Ft. Wilderness and another boat that runs from the Contemporary to the WL. Each boat has a different colored flag on it (although I forget which flag goes to which resort!) Sorry about that!
You can use this <a href="http://216.205.78.253/asp/twiz.asp">transportation calculator</a> to get a good idea of the travel times.