Yea you want an isolator since you don't want the trailer batteries dragging down the engine battery.
Your big problem is voltage drop. To get a battery fully charged you need to get it up to 14.4v or more. If that's what your alternator puts out, then you use too small a wire you'll end up with less - maybe a lot less - at the other end of the wire, and your trailer batteries won't ever get a full charge. That will shorten their life.
Diode type isolators, like the ones you see in the auto parts store with the heat sinks, aren't very good since they have a 1/2 volt or more of voltage drop right off the bat, and then you'll lose more down the wire.
Solenoid setups, called a "split-charge relay" are the way to go.
Then you need wire that is big and fat enough to get the power all the way to the back without dropping the voltage too much.
So, from the engine battery, to the solenoid, to the big fat wire to the back to the trailer batteries. You wire the solenoid so that it is energized when the key is on "run" (not accessory) and that ties them all into one big battery whenever the engine is running and everything gets charged.
EDIT: Oh, and use a big fat negative wire as well. A pair of heavy jumper cables with the clips cut off would be about right.
