As an aside to this thread, I am probably going to run a little thermo-electric cooler and some fans in the van for camping, and I don’t want these to discharge the starting battery, so I was going to wire in a few extra batteries into the back area of the van under a box of some sort. What is the best way of going about this effectively?
If you want these to charge off of the alternator, you may need to put in a bigger alternator.
Then, you can put in a relay that is connected to the “run” wire, so that it is closed when the vehicle is running - this will let the batteries charge, but will disconnect them when you turn off the ignition, preventing your load from discharging the starting battery.
The alternator on the car is 100 amps, I figured that it would be big enough? What do you think?
Probably, but you need to measure your maximum current draw to be sure - turn on your lights, AC, fans, etc. and then measure how much current is being drawn when charging all your batteries. It may be easier to measure each circuit independently and add them up (100A DC meters are hard to find).
BTW, the symptom of an undersized alternator will be a dead alternator - you will fry the regulator or rectifiers.
Sweet. Can I use any relay or how would that work?
You need a beefy relay - auto parts stores carry them. Figure on at least 50A.
So, you wire your new batteries to the load, and then use the relay to interrupt the charging circuit from the alternator to the new batteries. Does that make sense?
Yeah that makes sense. So the relay is going to have a ground? There should be a small wire that is hot when the ignition is, and then the main wires to the main battery? Sort of like a starter’s solenoid?
Hard to draw a schematic on the SDMB.
You have a lead from the “run” circuit going to one terminal of the relay coil.
The other terminal of the relay coil goes to ground.
One terminal of the relay contacts (Normally Open) goes to your alternator (or the Plus terminal of your starting battery).
The other terminal of the relay contacts (the Common) goes to the Plus terminal of your new batteries.
The negative terminal of your new batteries goes to ground.
I am sure I could probably figure it out based on the instructions from the relay.
It sounds a lot like an amplifier for a stereo system. There is a remote wire that tells the amp when the ignition is on, but the amp is wired directly to the battery. When the remote wire is hot, the amp turns on. Its the same principle, right? Except nothings turning on but the actual charging circuit?
I appreciate your patience Beowulff. 
Yes.
There’s one other thing to think about - You might want a manual interrupter switch in the relay coil circuit. This way, if the new batteries are really dead, you can manually disconnect them, so they don’t load down your starting battery when you try to start the vehicle. After it’s running, you can turn the switch back on to charge them.
A manual switch (low amp, for the relay) in addition to a relay is a good idea, but my suggestion is to consider a manual switch (high amp, for the batteries themselves – some examples at the top of this page) instead of a relay. This type of switch is more reliable than a relay, and gives you the option of connecting all the batteries together any time you want to. For example, this would give you a built-in jump start if the main battery went dead. The disadvantage is that you need to remember to turn the switch off when you want it off, but if you can do that it could save you from other possible problems, like a stuck relay.
You do not want the aux bateries in the circuit until the engine is running. A manual switch in series with the relay. One as a back up for the other. Also a normal lead acid battery when charging can give of H2, you will be better off with some type of jel battery.
Also you might want to consider a 120/12 volt rectifier added to your system.
Also take a look at the amp draw of the equipment you put in. I am not sure what the amp/hour ratting of batteries are today but I would expect around 200 HR. These days batteries are rated in cold cranking amps.
If I had a manual switch, couldn’t I just forgo the relay or would it be a good idea to run both?
Snnipe 70E, I hadn’t thought about the H2 venting. Thats a good point.
The disadvantage of using only a manual switch is: you are going to forget it at some point, and then you will end up with a dead starting battery. I would use both.
Use both. The relay then acts as an “oops I forgot to turn off the switch” safety.
a manual switch inside the battery compartment is good. if you remove batteries or are doing work it then prevents your cables and connectors from being energized by the relay accidentally or mistakenly.
a starter battery (cheap and available though not the best for storage battery use) can weld metal if shorted and so you want to be able to positively isolate this circuit from your starting circuit when doing work or wanting one not to affect the other.
I thought about putting this solar charger into the system as well, I would need to relay this in as well, right?
Also, I wanted to double check my math: 15 watts @ 12 volts = 15/12 = 1.25 amps. This is right, isn’t it?
How about a battery isolator? Pretty common for RVs. Allows the extra batteries to charge from the alternator, but won’t let accessories drain the main battery.
I’ve done this for mega stereo systems too.
I was thinking about getting one of those premade battery isolators but I think that they are mainly just a relay and I can get a 60 amp relay for about 5 dollars, or I would need to spend about 40 bucks on an isolator. I am looking at both too. If I was to run two deep cycle batteries, how big of an isolator do you think I would need, retterath?
Thanks for all the replies!