I decided to mount my battery in the left side of my car. Preference I suppose, doesn't really make a difference unless you're a perfectionist and want it in the middle.
Ran the 2 gauge wire under the drivers seat area, and out the firewall hole.
Ran the 4 gauge wire the same way, and out the hole.
Disconnected old battery, and wires.

Now you have
-Positive wire to fuse box
-Positive wire to starter
-Negative grounded in the trunk

Connect the 2 gauge wire either directly to the starter, or to the connector the old battery terminal used, you will need to re-crimp a connector if you would like to hook it up directly to the starter.
Connect the 4 gauge wire the same way to the fuse box lead.

Drill a hole (Or use an existing hole) in your trunk. I used a 5/16, with a fender washer, nut, and lock washer right below the box, in the lower left corner.

That's it, other than connecting the two wires to the terminal at the battery.

By the way, I used standard hardware store 2 and 4 gauge. This was not very flexible at all. It was enough to mold underneath my seats, it will take some pressure to get the wires to set. If you don't want any hassle, you can always pick up some high-performance stereo wire for about $3-$6 a foot, mine was only around $.70/foot.

8/19/00

Well my original battery box failed. It cracked and broke in more places than one. So this time I made sure to secure my battery so that even SCCA officials would be proud.
I bought a $6.99 Wal-Mart Marine battery box, J-hooks, and a battery hold down kit. Total: $13.00.