Hrm...I think I made a mistake then. I placed the Thermal breaker before the bus bars behind the helm console (accessed via the access panel). moving it close now makes perfect sense and is an easy move. I'll have to provide the before and after pics (at least of the battery side as I'm still not 100% happy with the helm side look, but I know the wire is good and up snuff).
With regard to your question about the bilge pump circuits, I would highly recommend that the bilge pump circuits that have a float switch on them should be connected directly to the battery, or to a terminal that is always hot regardless of the battery switch positions. Otherwise, a blown fuse or circuit breaker could result in disabling the bilge pump float switch, and a leak will eventually result in a sunken boat...