It is pretty standard in a 3 battery setup to wire 2 batteries together as the "house bank" and one battery kept separate as the "starter". The three are then typically wired to a 4 position switch with off, bat1, bat2, and both as te 4 positions. This lets you run your house batteries without fear of runing down your starter and lets you use your house batteries to start if you should ever have te starting battery fail. There are also more complex alternatives to this that are even better...check out:
For a pretty good run down on thhe options.