These instructions were written by someone on a VW email list I'm on. They're pretty good so I thought I'd put them here. They're a little VW-o-centric, but the principles should be the same for any vehicle. If you have any questions, email me and I'll forward them to the author.
How to hook up an auxilliary battery in your car:
You must hook the new battery, the old battery, and the generator (or alternator) to either a battery ISOLATOR or a battery SEPARATOR. An ISOLATOR is a box about the size of your fist with cooling fins on it. They contain two diodes which eat .7 volts apiece--for this reason, you should not use an ISOLATOR.
A SEPARATOR is basically a relay. It looks like a small cylinder about 40mm across and 60mm long. It does eat 1 amp., but only when the engine is running. Starter relays, from a Ford for example, will work, but eat up to 3.5 amps. My SEPARATOR cost me US$19 at a hardware store.
When you find a SEPARATOR, here's how to hook it up:
Leave the wire from the generator/alternator going to the starting battery. Leave the wire from the starting battery to the starter. Disconnect the BIGGEST RED wire from the starter that goes to the front of the bus, connect it to one of the big terminals on the SEPARATOR -- either one. To this same terminal, connect a 10ga (6mm)wire to the positive terminal on the new battery. Connect a 10ga. (6mm) wire from the other large terminal on the SEPARATOR to the place on the starter where you just removed the BIG RED wire. Connect a 16ga (1.5mm) wire from the small terminal on the front of the SEPARATOR to terminal 15 on the coil--the one with all the black wires on it.
Now, when the engine is running (or the key turned on) both batteries are connected, and so will charge. Accessory power will come from the gen./alt.. When the key is off, accessory power will come from the new battery only.
The starting battery will remain fully charged to get you started when you're done hangin' around.
The best place to mount the second battery is opposite the starting battery. There's a nice space for it to go, and it will be close to the things it needs to be connected to.
There are two types of batteries that we are likely to put in our busses, starting batteries, and deep-cycle (marine) batteries.
Automotive starting batteries are only designed to cycle about 10% of their total capacity, and to be recharged quickly from the generator/alternator. They will be ruined quickly if cycled more deeply often enough. They are great to start your bus, but not for running anything very long with the engine off.
Deep-cycle batteries are designed to cycle up to about 80% of their total capacity. Their capacity is rated in amp-hours. This rating is generally based on a 20 hour rate, so if the battery is marked 100 amp-hours, then it will provide 5 amps for 20 hours (without recharging). They should not, however, be drained below 50% of capacity very often, unless you want to buy a new one. In any case, they will not usually last more than a few years at most. You want a deep-cycle battery to run your stereo, interior lights, computer, fridge, etc. when your engine is not running.
You do not get out what you put in For every amp-hour you use, you will have to recharge about 1.25 amp-hours to return the battery to the original state of charge. So take the amperage of your gen./alt. minus whatever you are using while you drive (headlights, stereo, etc.) to figure out how many amps you have left over for charging your auxiliary battery. If you are on the road for a few hours per day, there won't be any problem, but if not, you only have so much power to use!
Sorry to be so long-winded, if you have any more questions, just ask.