my understanding of the situation is this:
In order to charge a battery, the alternator produces a "high" voltage of up to around 15v for a discharged battery. To float it along and run your car's electrical system, the alternator produces around 14 volts (14.2? 13.8? something like that) I could be confused, it might only be 13.4v. But regardless, your alternator doesn't put out "12" volts unless the battery is depleted far enough or the load is high enough that it can't produce the higher voltage.
I found the following table at
The 12volt Side of Life (Part 1)
So if you have two batteries in your rig, and one is older and charges more slowly/incompletely due to have sulfation or cracks or low electrolyte, (etc etc), then the alternator is going to try to get the lower battery up to 12.9v. But it will be charging both batteries. So when the fresher battery is fully charged, it is going to continue to receive higher voltage than it needs, thus boiling off electrolyte and generally overcharging the battery.
I'm not an expert, I'm just regurgitating what I've read on the subject.
I have run two batteries as described- no isolator, just the two batteries. Battery life in that setup wasn't good.
My favorite way to run dual batteries is still the following:
Leave your entire stock system alone, minus the stereo, disconnect that completely from the stock system.
Add a second alternator. Add a second battery and connect the positive to the alternator, the negative to ground. Put all of your aux. loads on the 2nd battery/alt (also add the stereo to the 2nd battery/alt).
It is a hassle to add the 2nd alternator, but other than that, the system is really painless and does a great job of addressing the issues for which most people want a 2nd battery. It should also make your winching/offroad lights/fridge work better as you've got more available amps coming off of the 2nd alternator because it doesn't have to run the engine, fan, headlights, etc.
One thing: you've got to be very careful with wiring stuff so that you don't ever cross the positive wires, or you'll end up with the situation that I had: two alts charging two batts and killing them off quickly
If you want to get fancy (I wouldn't) you could add in a marine switch such that would allow you to connect the two batteries for very heavy loads like winching, or for starting the truck if the stock battery goes dead.
But part of the beauty of having the batteries completely isolated is that you can't flatten your starting battery by winching off of it.
Side note: you can get an inexpensive alternator for about the same amount of money you would spend on an isolator/switch/wiring/lights/etc system. So the bracketry is about the only obstacle to doing the dual alts
Shoot, I don't even need dual batteries and I'm getting excited about doing a dual alt/batt system
