I've taken the Contemp, FW, WL boat more times than I can count over the years. It seems like most times they'll keep two boats running in opposite directions:
Contemp > WL > FW
Contemp > FW > WL
If both boats look to be coming in around the same time, you can check to see where it's headed next. Otherwise just jump on the next boat that shows.
At the the Lodge and Ft Wilderness, they also have a separate boat route that runs to the Magic Kingdom, so if heading back to the Contemp, make sure you're on the correct route.