Go to
eBay, search "KnuKonceptz" and buy, say, 30ft of 1/0ga wiring. Trust me, it's much better to start with 1/0ga than it is to start with 6ga, then tear it out and run 4ga, then tear it out and run 2ga, etc. Now here's what you need to do...
*Run a strip of the wire from the battery that is used to start the car (not your extra battery) from the (-) terminal to a good ground on the chassis, as close to the terminal as possible.
*Run a strip of the wire from the same battery's (+) terminal to your alternator's (+) terminal. It never hurts to fuse this wire, but it isn't necessary.
*Run a strip of the wire from a ground on the chassis to a ground on the engine block (you should already have one, just with much smaller wire). You can either replace it with the 1/0ga, or just add the 1/0ga in the same spot. It won't make a huge difference, but it isn't a bad idea.
*Run a long strip of the wire from the same battery's (+) terminal to the extra battery's (+) terminal. It is very important that you fuse this wire.
*Run a short strip of the wire from the extra battery's (-) terminal to a good chassis ground.
You may hear people talk about the "Big 3 Mod", and the first 3 steps I told you are what it is. I highly recommend you do it, because it will let the alternator "breath", so it will likely pull around 13.8v instead of 12.8. This is actually better on your alternator, because it won't be straining to pull out the required volts. It also is easier on your amp for a similar reason.