There is a shuttle boat that takes people to Fort Wilderness. The dock is located near the entry ramp for the monorail. Be sure to get on the correct boat, as there are boats that go to other resorts as well. I don't remember how long it takes to get from MK to FW, and then there may be some travel time between the dock at FW and Trail's End.
The little launch closest to the monorail actually goes to the GF and Polynesian. Walk to the docks straight ahead when exiting the MK and look for signs for FW and WL. The boat you'll want goes to both. I would allow 30-40 minutes although you may make it faster than that. Once you're at FW, it is a very short walk to the building that houses Trail's End and also the Hoop.