Hi Will,
I put my starting battery under the aft berth. My intent was to put an access panel above it, but I never got around to it.
I mounted a battery switch inside the engine compartment door. The switch is exactly like the switch mounted near the nav station. The switch allows me to charge the house batteries and the starting battery, or the starting battery alone, or the house batteries alone.
I don’t remove my batteries during the winter. Instead I run my battery charger on a timer and charge for a few hours once a week, so not having easy access to the starting battery isn't a big problem.
I installed the Frigoboat refrigeration system with the keel cooler. It doesn't need a water pump to operate. It's very efficient and I've never had a problem with using the two house batteries. That said, our boat is on Lake Superior, so I'm not totally sure if systems operating with warmer water temps would experience the same efficiency.
Enjoy,
Bob