I have decided that I'm going to build the JayBee's walls straight up from the sills--so the bottom plates of the walls will be screwed directly to the sills. I'm going to put the floor joists inside the walls, instead of under them. (Except for the bumpouts on the east and west walls--those will have the walls on top of the floor.) This method will allow me to connect the vapor barrier under the subfloor with the vapor barrier behind the walls--creating a complete envelope. (I have plans to install two air exchangers in the space--to keep the interior air fresh, especially in the winter when the windows won't be open.)
I have also decided to use 2 x 6 lumber for the floor joists--so the JayBee's floor will be at one continuous height throughout the entire house. This will save me having to fuss to construct a platform along the north wall upon which to set the washer/dryer, refrigerator, and hot water tank.
Thank you, Dale, for helping me think through these things and make up my mind! Thanks also for the chain-saw lesson.