I guess the answer is, it depends. My father has an
ECV, and we've stayed at Fort Wilderness a number of times. You cannot take them on the smaller boats, you can only take them on the large boat. This is usually not a big issue, the times we have been there they are usually running two of the big boats. The only time we really dealt with long waits were when the Hoop Dee Doo lets out.
The crew is pretty good about trying to direct you. If the water level is high, they will load the people on to the boat, then ECV's. If the water level is low, they will probably load ECV's first. The weight of the people on the boat will raise or lower it slightly.
When you board the boat, there is a wall right in front of you, you can go around it to either side. One way leads into the boat towards the back, the other way leads towards the front of the boat. Most of the time we were directed to go to the front of the boat, and he would park his ECV right there. You can easily fit two there. Occasionally we have been directed to go towards the back of the boat, there is plenty of room there.
The maneuvering can be a little bit tricky, but my father generally found it easier than the buses. They don't tie them down on the boat, so you don't have to get it into the perfect spot like on the buses. Also, much of the time you load from one side of the boat, and exit from the other. So you drive in one door, and when you get there you drive straight out the door on the other side, without having to back up.
Hope that helps!