Simple.

One battery (bank) hooked up to start the engine and the the engine
alternator charges this bank (normal wiring).

Two battery (bank) hooked up to run whatever you want.

Battery combiner (West Marine Catalog) hooked between the two batteries.

When the battery voltage on either battery rises above the cutin voltage of
the combiner the batteries are connected and BOTH charge. When voltage
drops below the cutout voltage of the combiner the batteries are
disconnected.

Complex (my boat)

Starting battery, one group 24, for main engine, stock engine alternator
charges this battery.

Starting battery , one group 24, for generator, no direct charging.

House battery bank, 8 Trojan deep cycle batteries, 880AHr, charged by, 1)
130A alternater on main engine 2)100A alternater on generator, 3) 400Watt
wind generator, 4)400+Watts of solar panels, 5)100A battery charger in
inverter.

Three battery combiners, Main starting battery to generator starting
battery. Generator starting battery to House batteries. House batteries to
main starting battery. Note multiple paths. This was not by plan, I
accidently purchase three combiners and decided to install them all. Only
two were needed.

Battery switchs used in emergency starting and charging. Main engine,
starting battery and house batteries. Generator, starting battery and house
batteries.

Everything on the boat except for starting the engine or generator runs off
the house bank of batteries.

Mike