I did a lot of rewiring on my GB42 when I had one, primarily after I added two sets of golf cart batteries behind the two main engines to make a "house" bank. Yours sounds like how I inherited mine; three batteries with one for the generator while the other two had an automatic paralleling relay to send their combined power to which ever engine was being started. The poor thing about this was the fact that at anchor, I was using starting batteries to power the house loads hoping that they would not be depleted when it came time to restart the engines/generator, assuming you don't use the genny overnight. I would guess that your third battery (generator?) has no interface with the 1-2-both-off switch, and that it is just the two main engine starting batteries which got to the 1 and 2 posts on that switch. Unless you have a reliable drawing, you will have to trace the cables. The battery switch you describe, if it was like mine, is just for house loads and does NOT interrupt the circuit between the alternator and the batteries; so, despite the fact that it has a warning on it not to shut it off while the engines are running (in order to not blow the alternator diodes), you probably can, but test the circuit first with the engines off. The big battery disconnects which you should find in the engine room very well could interrupt that circuit - again, test it.
Leaving the battery switch on ALL offers the opportunity for a dead cell in a battery to drag the other two batteries down with it. Since the starters are independent of this switch, you don't need it in other than 1 or 2 most times which lets them remain separate. I added a second battery switch which allowed me to select the third battery into the mix for house loads should the loads demand.
If you ever want a look at my final design, send along a private message with an email address, and I'll send along a .pdf file.
