I see this issue on wiring a remote battery come up frequently so maybe I can help with ideas and specific recommendations.
*************DISCLAIMER***************
THIS IS NOT THE ONLY WAY THIS CAN BE DONE!! THIS IS THE WAY *I* DO IT AND I CAN GUARANTEE THAT FOLLOWING THIS METHOD WILL GET YOU THROUGH TECH IN SCCA, NASA, LEMONS, CHUMP CAR, AND NEARLY ALL ROAD RACE SANCTIONING BODIES. IF YOU DON'T LIKE THIS METHOD THAT'S FINE, DO IT YOUR WAY, I HAVE NO PROBLEMS WITH THAT. IF YOU CAN'T READ A WIRING DIAGRAM OR DON'T UNDERSTAND BASIC ELECTRICAL CONCEPTS THEN DON'T ATTEMPT THIS BY YOURSELF!!! IMPROPER WIRING OR USE OF THIS ADVICE CAN CAUSE SERIOUS PROPERTY OR PERSONAL INJURY SO DON'T BLAME ME IF YOU SCREW IT UP. 
*************END OF DISCLAIMER**************
Now with that out of the way, let's begin. The first thing you need is a kill switch approved by your sanctioning body. I use the 4430 switch from Pegasus Racing (
http://www.pegasusautoracing.com/productdetails.asp?RecID=1464 )
(This switch as I understand it is not legal in NHRA. Why, I don't know, I'm not a drag racer and don't have a copy of their rule book.)
You can find this switch other places as well (HRP World, Racer Parts Wholesale, etc.) but it will be a very similar switch. Watch out for low quality chinese knockoffs, you get what you pay for when you're switching a couple hundred amps. The important thing is that it have 6 poles. Two heavy, main battery NO poles. Two spade terminal NO poles. Two spade terminal NC poles. Now on to the wiring, it's really not that hard.
Here's the basic wiring diagram:
OK, on to specifics.
1) Battery Cables: I use Veri-Flex #2Ga Welding Cable. This is insulated for 600V, -40°C - +90°C. It is very flexible and has very fine wires and can easily carry anything your battery can deliver through it. One cable comes from the positive terminal of your battery to one of the heavy poles on the switch. These are 3/8" and you'll need some good quality copper lugs for the #2ga cable. I get mine from Fastenal. The other heavy cable runs from the other heavy pole on the switch directly to the starter. I also run a completely separate ground wire from the negative pole on the batter to the engine block or head itself. Make sure wherever you terminate this the area is clean and the paint is removed. I also use a star washer between the lug and the block head to make sure there is a good connection. In addition, I run a lighter gauge braided ground strap from the negative pole on the battery to the chassis somewhere near where the battery is mounted and another similar strap from the engine block to the firewall up front. You can't have too many grounds or too good of a ground.
Now we get to the interesting part, making sure when we flip the switch it kills the engine.
You are going to need a length of wire that will run from the switch to the igniter. This is not a single wire but is a three conductor, 14 ga wire. I use Standard brand electrical wire in a gray sheath that is p/n C14-3E. This sheath is very abrasion resistant and rated for 105°C. It doesn't matter if you're running a turbo car with DIS or a N/A car with a dizzy, both use an igniter. Find the wire that is switched on from the key to the igniter, near the igniter because you're going to cut that wire in a minute.
The wires are colored Green, Black, and White. The colors really don't matter which you use but I use the white and black to go to the igniter. Properly crimp female spades onto the two wires and plug them into the two terminals on the kill switch that are Normally Open. At the other end by the igniter cut the ignition wire and again, properly crimping or better still, soldering and heat shrinking, one end of each wire on the two ends you just cut. Now, when the switch is off, both your battery circuit is open and your ignition circuit is open.
What is the other circuit for? Glad you asked. When you interrupt the battery circuit like that the sense to the alternator reads "0" volts. On SOME alternators this can cause a huge output spike very briefly and has caused issues with popped electronics. Before some say this can't happen, I used to think that as well right up until I popped two PCM's for the Cadillac Northstar in our race Fiero. It CAN happen, especially if the electronics are old with tired caps in them, so we're going to stop that from happening.
You still have one more wire coming out at each end, the green one. On the engine compartment end, properly crimp a ring terminal that will fit the stud of the main power output on your alternator and put that wire there. Put a female spade terminal on the other end by the switch and plug it into one of the two remaining male spades on the switch. You have one more connection to make. Wire the supplied 3 ohm/11Watt resistor into a piece of wire long enough to reach your braided wire that you installed from the battery to the sheet metal in the trunk area. On one end put a ring terminal that will match the terminal on the braided strap, the other end will have a female spade connector that goes to the switch.
DOUBLE CHECK ALL YOUR WIRING NOW BEFORE YOU HOOK UP YOUR BATTERY!!! IF YOU HAVE THIS HOOKED TO THE WRONG SPADE TERMINALS YOU WILL HAVE A DEAD SHORT!!
With the master switch OFF go ahead and hook up your battery. Watch for any sparks or signs of an electrical contact as you do. If you have ANY sign of spark, you have something wrong. If all is good, hook up the battery properly. Now watching very closely, turn the master switch ON. Be ready to turn it off instantly in case you have something wired wrong. If all is still good, start the car. Everything should work as normal. With the car running, switch the master OFF and everything should be dead with no sparks or bad things happening.
You don't need to mess with the alternator wiring at all beyond adding the single grounding wire to the main alternator/battery feed.
What you're doing when you flip the switch is first it interrupts the battery and the ignition power to the igniter opening both of those circuits simultaneously. At the same time you are closing the circuit from the alternator feed wire to a ground through the resistor dumping whatever spike there may or may not be for that millisecond to ground protecting your electronics.
Hopefully this is clear enough to follow. As I said, there are other ways to do this but this is an approved method for most road racing sanctioning bodies and it will work safely every time if you wire it properly.
John Stricker
Russell, KS
