Most RV and boating supply stores sell a "battery isolator relay" for 20-35 bucks. The two contacts this relay can be connected between the positive terminals of your starting and auxiliary batteries. The relay coil can be connected to the "run" position on your ignition switch, so that the coil is only energized when the engine is running. Finally, the negative post of your auxiliary battery is connected to chassis ground, same as your starting battery.

RESULT: Both batteries are connected in parallel whenever the engine is running (thereby allowing the alternator to charge them both), but isolated when the ignition switch is turned off.

This is the same scheme that most motor homes and many boats use - It's simple, and effective.