Hello Chris
I am sorry I cant answer your question fully with out a circuit diagram, and as there are different battery switches I would also need to know the type of battery switch as well and what connections the alternator has on it.
On an automatic system it is normal to charge both batteries at the same time by using split charge diodes. In some cases these can bypass the battery switch as they will only allow electricity to flow into the battery and not out. (however it may be advisable to put a fuse in the diode circuit.) These will work but in many cases will not allow the batteries to become fully charged (the 0.5v drop through the diodes will reduce the max charge voltage and the battery will only reach approximatly 85 to 90% of its max charge.) unless you have your alternator adapted or use an intelligent charger.
I use a split charge relay system and there is no voltage drop with these. I got it from a caravan accessory shop.
If you are not competent with boat and engine electrics I would advise asking someone local who is.
Mike
Mike Edwards
Seal 28 "Aztec"
Mike Edwards
Seal 28 "Aztec"