Re: Which battery?
A lot of personal choice here.
The way my boat is setup is everything needed to run the boat is hooked to the starting battery.
Starter, Bilge Blower, Bilge Pump, Navigation lights, Horn, Windsheild wiper, Trim tabs, Compass.
All the add on gear is on the deep cycle.
Loran C, GPS, Fish Finder, VHF, accessary plugs.
On my boat if the motor is running everything gets charged thru a battery isolator even if the second battery is not on board it would all work when the motor is running.
The gear on the starting battery is usually only on while running and the stuff on the Deep cycle can be on while drift fishing, anchored, or pulled up to the beach but it will not drain the starting battery while the engine is off.
This is not right way or the wrong way, it just my way.