Vehicle has three batteries, is there a way to isolate the crank battery from the compartment batteries?

It actually should have one already if it has a shore power charging system in it. The isolator is normally part of that unit and allows the engine to charge the house batteries while the engine is running, and it charges all of them when plugged in. When the shore power disconnects the isolator splits the system automatically using the relays in the charger/inverter unit. Now if that unit was removed there should still be an isolator under the hood. It's usually a box with 3 terminals on it. One connects to the house battery bank; one connects to the cranking battery and the other goes to the alternator output.
Who made the unit? Most of the companies can get you wiring diagrams for the stuff they add, just won't have anything the squads added themselves.

That is a different layout than they normally use. Most of the units I've worked on have a starting battery under the hood, the house batteries are normally in a different location. In your case I would probably add a different battery in another spot. Then set that one up as a starting battery. It would allow you to use a common isolator to split the systems and still charge the batteries with the factory alternator. You could do that with the current batteries but it's going to take running new cables to one battery to split it off and installing a heavier cable to run the starter. An RV store would have all the parts.