I can't help with the placement per se, but up front would be my suggestion, seconded by opposite of the starting battery at the stern. Batteries are heavy, but operating with two would allow for a smaller starting battery. How long and loud along with system design, or number of speakers, amps, sub, etc, will determine the size and construction of the deep cycle battery. Charging while operating boat could be achieved with a battery isolator. Shore charging I would recommend a two battery conditioner like the fishing folks use, great for storage as well. We like pictures of projects, good luck on yours.