Oh boy, this is getting more complicated than it needs to be.
The boat routes have been tweaked over the past year or so, so let's be clear on how things are now.
There are large, partially enclosed boats that take passengers directly back and forth from FW to the MK. These boats at one time were shared with WL, but no more. These boats do not stop at WL at all at any time of day. Just FW and MK. As you head out to the dock, the line to enter this boat will be to your left.
There are smaller, open boats that travel between FW and the Contemporary Resort and Wilderness Lodge. These boats make a loop from FW to those resorts. These boats do not go to the MK. Sometimes they go to the Contemporary first, and then stop at WL, and then head back to FW. Sometimes they go the other way and stop at WL, and then the Contemporary, and then back to FW. I have not yet been able to figure out the rhyme or reason as to how they determine what resort they are going to first. I don't know if it is adjusted by time of day, or based on demand. But, you certainly can ask the boat captain, and he or she will tell you. If the boat is heading to the wrong resort for you first, you can ask the captain whether you should board, or wait for the next boat. I believe that at certain times of day, all the resort boats follow the same loop, so you may have to visit the other resort first anyway. The resort boat line is to your right as you head down the dock.
As far as catching a boat from WL to the MK, the WL has its own dedicated boats for this purpose, just like FW. Those boats go back and forth from the WL to the MK only, no other stops.
I don't worry about flag colors. It used to be important, because there were different routes run by similar looking boats. I don't even pay attention to flag colors any more. There is a MK boat and a resort boat. That's all you need to know. It is simple.
Good luck.
TCD