Paul
How do you keep the aux battery charged - is it possibly as simple as running a wire from one of the busses to the aux battery with a diode in between to stop the juice from flowing out of the aux battery during start up?
In principal, yes. In practice, the Aux battery dioded of the main battery bus with a resistor in line to keep the curent down to a reasonable level. You also want a diode with as low a forward drop as possible. This arrangement keeps the Aux battery charged trickle charged (not perfectly, but good enough) when the aircraft sits, and tops it off when the Alternator is up.
Paul