Connect everything up and 'voilą!' You should now have some very nice smooth bass. Don't forget to disconnect the rear 6x9's so they don't muddle your sound. I used electrical tape to tape the speaker harnesses down so they wouldn't rattle. I recommend playing with the amp settings quite a bit before you mount it to the backseat. This allows much more ease of access. Also, remember to close the trunk each time you change something so that you recreate how it will sound as you're driving. Also, remember it takes several hours of moderate sound levels to "break-in" your sub so take it easy. I used my fader to control my sub output and faded to the front at F3. This allows me to push my front aftermarket components with minimal interference from the stock rear speakers.
In retrospect, I probably would have went with the JL 250/1 and W3 combo and save some cash. My current setup is more than I could ever use, but I'm still very happy with it. I have the '06 with Bluetooth, so I don't want to go messing with the front amp any time soon. I would like to add an amp there, but I'm waiting for some brave soul to replace the bose amp altogether and preserve all of the features of the Bluetooth phone connection.
Feel free to add comments or question my install. I will edit it as necessary. Hopefully this helps out someone who was in my shoes but didn't know where to start. Here's a link to some reference material that may be useful:
http://www.g35frenzy.com/forum/showthread.php?t=1044
