1---I think running dual batteries in a car is silly. You still need enough alternator to charge them, so if the alternator cannot keep up, you need more alternator NOT more battery
The exception to this is if you are one of the irritating people who shows up in a park/ beach, opens the doors, and turns the stereo up with the engine off
2--PLEASE do NOT run a 3 terminal solid state "isolator." These have failed in a number of marine installations, and in THREE cases I know of specifically, were the cause of a bilge explosion. Here is how they can fail in a dangerous mode. Isolators are nothing more that two large diodes. The MAIN battery diode is usually under the most strain and can fail OPEN With a conventional "sensing" regulator, this means that the MAIN is NOT getting charged, and the regulator says "hey, the battery is going low, let's charge!!!!" So the regulator ramps up the charge voltage, and the regulator/ main battery sees none of this because it is now disconnected from the alternator output!!!
But the alternator is charging the LIVING HELL out of the auxiliary battery!!! The voltage is going HIGH, the battery is bulging at the seams, and things are NOT good!! What I'm referring to is one like this, again do NOT use these
If you want to use an isolator, buy what is known as a "continuous duty solenoid" These look vaguely like a Ferd starter solenoid, except they are designed to be powered, well, "continuously." AND these are what Rusty is referring to in his diagram above.
Just hook the two hot leads of the two batteries to the big studs, wire one of the small terminals to ground, and wire the remaining small terminal to switched ignition