On my 325, that part of the DC wiring is not included in the documentation either. I have not tore the boat apart to see, but I have two engines and two batteries, and I am quite certain that both alternators are connected together. Whether they are directly connected or connected through a diode isolator I cannot tell as I have not looked. But I have never liked that setup at all.
But adding a dedicated house battery is one project I want to do some day. If you find out if the alternators are indeed connected directly together, please post here as I'd like to know.
The conventional wisdom of using the 1-both-2 battery switch is on day one, put the switch on battery 1. On day 2, put the switch on battery 2. On day three, go back to battery 1, and so on. If you put the switch in both, battery 1 and 2 will be simultaneously charged by the engines, but both batteries will also be simultaneously discharged if you forget to take the switch out of the both position when the engines stop.
This setup would normally be a good candidate for the addition of a battery combiner so that both batteries can be charged by the engine(s) without risk of discharging both batteries, but in this instance, its probably better to correct this rube-goldberg setup first.