I'm starting to get my car hauler finished up and having never owned any type of RV (I'm a tent guy) I've not had the joy of installing a battery isolator. I can't see a point running the 3K winch on the trailer off the truck and I won't spend $60 on the junk breakaway kit so I picked up a battery box and full size deep cycle for the trailer that will run both the winch and breakaway switch. Now to keep that battery charged I need to install the isolator. I have an older diode type that I'm going to install, the issue I'm trying to figure out is this. My truck has dual batteries from the factory, they are wired in parallel. Can I attach the isolator to the alternator then run it back to the trailer battery and call it good without disturbing my existing factory charging system or do I need to run my primary truck batteries (HUGE marine deep cycle/starting) off of the other side of the isolator? Can a diode isolator withstand the draw of the 2 existing truck batteries if I have to tie them in?

Diode-style isolators Work well. They have a drawback, though - they keep the "Isolated" battery/batteries at a bit lower voltage (.7 volts lower). So the Primary battery/Batteries on the Vehicle should be on the Alternator side of the circuit. The AUX battery/Batteries should be on the "Isolated" side of the circuit.

Be sure to mount the Isolator where it can cool - high currents lead to high temps at the Diodes, and they will live longer if they are kept cooler.

I prefer Relay style isolation. I rigged mine to provide emergency back-feed for starting, should the Mains go flat. Additionally, the Relay style does not keep the AUX batteries at less than full charge. This is especially good when the AUX batteries are larger than the mains.

So would it be viable to just add the input to the isolater to the output of the alternator leaving the existing wiring intact and have the isolator feed just the aux battery on the trailer? I wasn't concerned about the voltage drop, I figure if my tiny alternator and battery on the ATV can keep an identical 3K winch running then a full sized deep cycle can do it alone. The max distance something would even be winched is 20'.

Yep - that would be the way to do it. Don't forget Fusing. Rather have a fuse protect the Car, rather than the Car protecting the Aux batteries!

Call me anal but I have self resetting breakers on all the trailer wiring, a 50A for the power supply to the trailer and there will be another 50A for the charging circuit. The constant hot to the trailer runs the 2-100W lights for loading at night and the charging circuit will keep the battery up for the breakaway and the winch. Thanks for the answers Handload.

I would go for at least a Main breaker that is Manual reset - don't want to have it reset after it was already smoking something, and before I could find the problem/let it cool/put a meter on it!

I have all the lights on an auto resetting breakers so when (and there has been) a problem they trip and stay that way until incoming power is removed. The charging circuit for the battery will be on a 50A maxi fuse, I paid $250 for my high amp alternator and I'm not going to fry it because I was lazy.