You can sign up at any of the marinas but once you sign up, you can only use that marina. Most people choose signing up at Wilderness Lodge because it has the biggest lake but it would be much more convenient for you (Eeyore2U) to sign up at Boardwalk or Yacht & Beach Club. (I know there are bikes at BW but I can't remember if there are boats there.)
Here is a link to a thread with more detailed info: Bike and Boat plan?
I don't believe BW has a marina. BC, YC, and BCVs has a marina right across the lake. It would be interesting to see how that works for Bikes and Boats at that location.