We stayed at Old Key West a couple weeks ago. The boat schedule was a MESS. It took us two hours to get from the marketplace side of downtown Disney, so we stuck with busses the rest of the trip.
What I understood was that the only place the boats dock is the west end, near cirque du soleil and Disney quest. From there, you have to take another boat to get to your destination.
So if you want to get from SSR to OKW it's two different boats. It's also a transfer if you want to get to the east end if DTD.