To charge both batteries "no matter what" would require the use of a battery isolator, really simple dealio tha "splits" the charge circuit like a cable TV splitter, well, sort of...
The charge wire of the alt. goes to the center post of the isolator, battery one goes to one side of the isolator and battery two goes to the other side Viola, now no matter what position the switch is in, both batteries charge and only the selected battery gets drawn on, unless of course the battery switch is in the "Both" position...
GT