What are you using? I've had very good luck with Blue Sea Automatic Charge Relay (ACR). It's a voltage controlled switch that combines that batteries when the voltage rises (like when the engine is running). When the voltage drops below the set point it separates the batteries. I've got 2 of them wired up on 2 different trucks. I haven't had any failures in about 6 years since I installed them.
Typically an "isolator" was the old diode based device that caused a .7 volt drop across it's terminals. This worked but really cut down on how much you could charge the batteries unless your alternator had external voltage sensing wires you could connect directly to the batteries. As far as I know the diode based isolator has pretty much disappeared from modern day installations in favor of an ACR.