In a battery switch scenario, all electronics, helm buss, amplifiers and alternator should be wired directly to the Perko switch common lug. There are few exceptions like a bilge pump/float switch for a boat stored in water. The stereo source unit, other audio electronics and amplifiers should never derive power from separate input sides of a switch as this can create noise and is potentially harmful to the audio electronics.
For preservation of your alternator, its recommended to use a voltage sensing solenoid (SurePower, etc) rather than a manual dual battery switch. But if your total batteries are going to exceed three Group 24s (one starting and two utility) then I would use a cascading scheme whether automatic or manual and gain an understanding of how to correctly manage the manual switches. Or, get an increased capacity alternator.
In any case, a multi-bank multi-stage smart AC shore charger is very important to battery longevity. You don't want to solely rely on the alternator. You need a charger with a capacity equal to or greater than ten percent of your total amp/hours. Plus, you'll need a method to isolate the banks while shore charging, and in particular to circumvent the solenoid isolation if applicable.
There's no such thing as a perfect charging system that corrects for everything. But you can come very close and in the process extend your play time at rest, protect your alternator from excessive loads and heat plus dramatically extend the lifespan of your batteries.
If you follow Brett's recommendation and run two total Group 31 AGMs, you can rotate your batteries or battery functions and extend them a little further.