Each lake has the smaller boats that run a circle around that lake.
The smaller blue flagged boat runs a circle from Contemporary to Wilderness Lodge to Fort Wilderness. When busy enough, two boats will run, one clockwise and one counter-clockwise.
A yellow flagged smaller boat does the same thing among the Polynesian, Grand Floridian, and Magic Kingdom. Again, when there is enough demand two boats will run, in opposite circles.
There used to be separate boats that ran from the Magic Kingdom to each of Wilderness Lodge and Fort Wilderness. But when we were there in January they had combined the route which made it long and crowded. I hope that was a January thing and they each have their own boat in the Summer.