If you're wondering where a given boat is headed on either Seven Seas Lagoon or Bay Lake just look for the color of the flag on the bow.
A green flag means it runs between the Kingdom and the Campground.
A red flag means it runs between the Kingdom and the Lodge.
A blue flag means it runs between the Lodge, Campground, and the Contemporary, there are two boats on this route and they run in opposite directions.
A gold(yellow) flag means it runs between the Grand, Polinesian, and the Kingdom.
I don't know if they still do it (it was always a rare occurrence) a combined red/green means it runs between the Kingdom, Lodge, and the Campground.