For the battery compartment staying dry, no they dont have to as long as they have a cover on them. Our pontoon battery is in the back right by the outboard motor. Where it is, it is constantly exposed to water and dampness, not like water is dirrectly on it since it is in the case but there isnt really a need to worry about the placement as long as it is not submerged or exposed to extreme heat.
As for the placement, maybe in another compartment.
good luck, hope this helps