Originally Posted by stevo
thanks jky. What position should I have the switch in when the engine is running? Can the engine charge both at the same time irrespective of any difference in charge needed by each battery?
In normal running, any position (except off) is fine. You will be charging whichever battery you have selected on the switch.
For starting, you select one battery or the other, unless there is insufficient power in either, then you select both.
When drifting or on the hook, select one battery or the other to avoid running both batteries down.
If you want to be able to isolate yet still charge both batteries, you need something like a "battery integrator", which is an electronic switch that connects the batteries when a charge voltage is present, but disconnects them otherwise. It sits in a parallel circuit delivering charging current to the batteries (the switch wiring remains the same, but charging current to an unselected battery gets routed through the integrator.)
That allows you to set your switch to, say, Battery 1, which will supply current to start the motor; yet when running, both batteries receive charge. Shut down the motor, and the batteries are isolated again. Your switch controls which battery(ies) gets connected to the output of the switch; the charging current takes a different route through the integrator to the unselected battery.
Another adantage of this is that you can't damage the charging system by accidentally switching to "None" while running, as the integrator is still connected to the batteries. Disadvantage is that it's harder to isolate the batteries to just themselves; you always have a very slight draw from powering the integrator (I think; you'd have to check the documentation of the unit in question to be sure.)
Lots of info on these units on the web.