Simple. The add a battery kit comes with a switch and a relay. The switch is basically 2 ON/OFF switches combined into 1 that allows you too select Off, On (normal condition both systems on but separate) and also 'Combine' for emergency combining both side together.

The Relay just goes between the 2 battery banks in series. 1 wire to start battery, 1 to house battery. The relay is just an open/close switch. When no charging is present, the relay is open, keeping both battery banks isolated. But when one bank sees a charge (either by alt or charger), then the relay closes, combining both banks so they both charge.
Only time you have to touch the switch, is if your start battery becomes dead and you wanna go home. This system works exactly how you plan to operate yours, but it does it for you. And you will have the same battery cables and battery banks with your plan, so it's almost a plug and play install.

Substitute the outboard motor for your I/O, Full install diagram. Ignore the ground wiring, makes it look too complicated

http://assets.bluesea.com/files/reso.../990170140.pdf

The reason I don't use something like this on mine is the battery bank (#2 on my switch) has two group 31 series batteries. After a full day of playing the stereo loud, they are both drained pretty good. The alternator cannot charge them from this state, it is too much of a load on it. I have actually lost an alternator by trying to charge the "house battery bank". I don't want the house batteries to be charged by the alternator at any time... So for me a switch works best. Seeing as I am going to ad a third battery to the "house bank" on my new boat, and I have outboards (probably not very strong alternators...). Going with a switch is the safest method for me.

I agree with ya there

So a couple questions now, first will my alternator charge three batteries back or will it hurt it? The second sounds dumb because I know that I have started my older big blocks off one battery without problem but I have always been told to switch to "both" when starting. So will one starting battery be sufficient?

Few things ugly....

If you have twins, you need a "field disconnect' so the two alternators can not "see" each other....otherwise you can actually end up with a burned rectifier bridge or a discharge situation.....especially because they are not externally regulated.

With a single, no worries. Consider your stock alternator as a faucet, and you stereo as a drain. If you can only charge at a rate of 85a but your 200w amp sucks 20a you are good. If it's a 2000w amp......system....you are pulling down at 2.5 x the rate at which your faucet can replenish. No chance to recover......unless you turn off the stereo.....and run for the computed time....eg: Two dead g-31 12v 770a batteries need just over 18hours to recover from a single 85a alternator at full field 100% efficiency. Those parameters although easy to read, do not exist. Variables like saturation, density and material type of battery (agm/lead acid) level above sea, gauge of wire, accuracy of termination connections, ambient heat/cold/humidity.....

You can see where this is going..... It is a perfect science, but the variables have to be know and considered.

Adding additional batteries acts the same as increasing the size of your drain without turning the faucet up. Sooner than later, you have no water in the tub (battery bank)

Adding a shore power charging apparatus helps, but not when you aren't plugged in....the same as your alternator(s) do nothing if the engine is off.

So.....look to adding a suitable source of power....then think of where you keep it. Also, having 2-banks is paramount......regardless of everything else I just typed

I'm running a perko switch with 2 battery setup. After parked run just the one for radio and the. Switch to both for back up and running.

I also have a perko with a 2 battery setup but thinking about adding a 3rd battery. So adding a 3rd battery and connecting it to the one that runs the stereo doesn't change anything? I have an onboard charger that I plug in when docked or in storage that completely charges them, but will adding the 3rd battery do anything when I switch the perko switch to both (all 3) batteries for any reason?

You will need to hook both batteries in parallel (positive to positive and negative to negative). This will basically make both batteries act as one. You should only do this if the batteries are the same model. It is also a good idea to not only make sure they are the same model but of the same age. What it will do is increase the capacity of that bank, but will also make it much more of a load on your alternator if this bank is run way down. Your on board charger will still charge them back up, but the charge time will double.

One thing to keep in mind, a high quality true deep cycle large capacity battery in most cases can be as effective, if not more, than having two smaller batteries. I run a lot of stereo power and for a long period of time, this is why I have opted for 2 house batteries and one starting battery. Most people will find replacing one of their batteries with a good group 31 or larger battery will provide more than enough power. Don't buy the hype of Optima batteries. Don't get me wrong, they are good batteries and serve a purpose, but for extended period of high draw service, they just don't live up to their cost. I use Deka AGM (absorbed glass mat) Group 31 batteries. I was considering looking a kinetic batteries for my new boat. Both of the batteries I have mentioned are true deep cycle "house" batteries, with Kinetic being specifically designed for hi-amp stereo systems.

yea i have already found the group 31 battery or batteries im going with, I have a 2 deka group 27 marine batteries right now and the stereo (2100 watts) usually last around 2 to 3 hours 60 to 80% turned up, so its either go to a group 31 or 2 group 31 batteries to replace one of the deka group 27 battery

So it sounds like two group 31s hooked to the stereo and then adding a third starting battery with the relay. Is this correct? I still would like some feedback on the alternator charging these up.

It sounds like my switch now a red Perko just switches the two batteries for charging, starting and off. My amps are wired direct to both batteries so they are not involved in my switch. I could put my amps on one good "house" battery and then have the other battery as a start battery. This would allow me to switch to the "house" battery when stopped listening to music saving my start battery. I then could switch to both to start and leave allowing both to charge. This sounds correct/thoughts? I don't need the Blue Seas relay until I add a third.