Okay, on the 7-seas lagoon on believe you have:
Big paddle wheeler goes directly from TTC dock to MK dock
Small boats (I think, am not sure) do a Poly/MK/GF route ... maybe two boats during busy times?
Bay Lake:
Small boats go between FW/WL/CR
Larger boat goes between FW/WL/MK ... again, two boats during busy times that go in opposite directions
Was this the question you were asking? I think you will find some of the routes adjusted based on how busy it is. Sometimes I see dedicated boats between FW/MK and then other times there are two boats that go in opposite directions.