The impedance on the stock amp is different than aftermarket recievers. I believe it is around 6 ohms. If you run the new cd player with the stock amp, you run the distinct possibility of shorting out one or more pieces (including your deck,speakers,or anything else you have wired to that system). So if you do, understand the risk. I am not saying it will definitely happen to you, but I wouldn't take the risk.
To bypass the stock amp, go to the local stereo shop and purchase the wiring harness kit. Make sure you specify you have the premium sound system. This makes installing the deck alot easier anyway. There is a second connector that should be listed as well, this one is for the amp bypass. You simply unplug the stock amp, then plug in the bypass connector. Takes about 5 mins.
If the bass is not enough for you, there is always the aftermarket!