I chopped out the factory amp and replaced it with the JL XD700/5. This amp fits in the same location as the stock amp. I also added a sub enclosure (2) 10" subs. The difference in sound quality/clarity is night/day compared to the factory set-up. I still have the stock rear decklid speakers which seem to be holding up to the increased power level.
You may want to check out subthump.com as they make a wiring harnesses that allows you to plug-n-play.