What I understand about battery switches is that the alternator will charge all batteries tied to the switch at all times. For that reason the switch must be capable of handling the output of the alternator, what ever it is. If the Alt has 80 amps then the switch must have 80A rating.

As far as harming the Alt, I wouldn't put it that way. More like over work the Alt, which could lead to premature failure, when comparing it's life to a system with fewer batteries. The output of the Alt is it's max rating but most of the time it does not work at this rate. When the batteries are low then the Alt will charge hard at first to bring the power level up, then taper off to a constant charge load of 10-18 amps. If there are more batteries and they put more of a load on the Alt then it could be held at a higher constant charge rate such as 50% of its total output or more. When this happens the Alt is running hotter and working harder which can make it work so hard that is does not last as long.

If I were to use multiple batteries on a switch I would also use a battery isolator for added protection. The isolator can manage charging to uneven battery levels with less heat on components and prevent switch failures from overload.

That is my .02 cents.

 

Why not just get a jump pack. This would save weight. I think 3 batteries for 1 engine is overkill. For the stereo You should get a capacitor. Depending on the wattage you are pushing I would get at least a 1 farad capacitor. The capacitor will save your batteries from the stress of the stereo. This would go between your battery and your amplifier. They also have voltage meters on them so you can see what your batteries have in them. I usually always carry a jump pack and it has bailed me out a few times from the stereo running the batts down. A decent jump pack will cost about 75.00 and will easily tuck away in a small space for when you need it. Also if anyone elses battery dies they can use the jump pack. Its a great item to have on the boat. Cheap insurance.

 

I use a starting battery and a trolling motor(deep cycle)
battery with a Perko 1-2-all-off switch in my boat. I
only start the engine with the starting battery. I run
the stereo off the deep cycle battery only. I never try
to charge the batteries with the "all" position. I take
my batteries home to "fully charge" them on a regular
basis. Since you have a killer stereo you may want to
get two deep cycle batteries. You will kill your starting
batteries by running them down many times. The deep
cycle batteries are made for that and will last a very
long time. You do need a different switch no matter
what. Don't run two batteries in series on one switch
circuit. I use 24 series batteries for my 502 MPI. You
may want to use series 27 or 31 deep cycles for the
stereo since you'll get more hours of use with them.

 

Another alternative to the capacitor........
http://www.kinetikaudio.com/default.asp

http://www.asinstallation.com/KineticBatteries.htm

 

Another alternative to the capacitor........
http://www.kinetikaudio.com/default.asp

Thats some cash there over a decent capacitor but yes that would work great.

 

Hookup diagram

 

Modified for a 2 engine 3 battery installation.
this allows a "ship battery" for stereo amps and isolation of the engines.
If you run the "house" battery dead you still have each engine battery.
If an engine battery fails you can select the house battery to start that engine.
If the house battery needs chargine you select ONE battery selector to "both" and that allows the alternator to charge the "ship" battery.

 

Or straight from PERKO instructions.

http://gator49.hostgator.com/~zeromyst/catalog/images/8501.pdf