Bill,
For what its worth, my gen sits in the second bay, and my fuse panel in the back bay closest to the axle. The 50 amp cord runs across the top of the bay from my genset to the panel. My back bay has a hole cut in the floor so I can drop my 50 amp (shore power) plug in cord out the bottom and still close the bay doors when parked.
I wouldn't be a big fan, of running the 50 amp cord from the middle to back bay under the bus, just seems like too much exposure. It was hard to tell from the post, exactly what you are trying to accomplish. But thats how mine is set up.