Originally Posted by al40
What you cannot and must not do is turn off both batteries (even momentarily) whilst engine is running... The alternator produces rectified DC but it's a nasty waveform that the battery supresses.
Be aware, however, that some engines have a spare wire in the harness for a "field disconnect", which essentially kills the alternator output while active. Marrying that with an appropriate battery switch will allow you to turn both batteries off while the motor is running (but not for long; no DC output, no power for the motor.) Intended, I believe, for switching through settings (i.e. from "1" through "off" to "2" for example.
I believe my F115 lacks this, but many motors do incorporate it. Would be a good thing to utilize, even if your switch is configured to avoid it, just in case some curious passenger decides to play.