As long as the subwoofer choice is well matched to the power of the in-boat amplifier's sub channel, a single amplifier chassis to run all in-boat speakers including the subwoofer is fine. The only instance where you really need to separate these two chassis is when your demand for power is large enough that it exceeds the capacity of a single-chassis, multi-channel amplifier. And with today's many large 5-channel amplifier options, that would have to be some really big power.

As you have already indicated your plans, you must separate the starting battery from the stereo battery/bank with an isolation switch in one form or another (whether manual or automatic).

If you are cycling your batteries really deep then a battery tender/maintainer/trickle/minder type charger isn't going to cut it for maximum battery longevity. Those are fine for maintenance in applications where the vehicle or craft is placed into storage with batteries already at a full charge.

When at rest, at the beach or otherwise, and you are listening to the system outside and away from the boat, the in-boat speakers (within the bathtub so to speak) plus their driving amplifier will have to work inordinately hard to project the sound at any range away from the boat and down at water level. It also tends to suck an inordinate amount of current and pulls your battery(s) down much faster. So try to leave this role to the elevated and directional tower speakers and turn the in-boats off to promote longer playtime and preserve batteries.

David