If you want to do a good job of adding an amp to your stock system, buy something called a PAC LC-2. The PAC LC-2 converts the high level audio signal (used by Bose amp) to a low level audio signal. You can use high level audio signals on some aftermarket amps, however the quality is never as good. The other advantage to the LC-2 is that there is a variable gain control on it so you can actually control the gain to the amp. The LC-2 is also quite simple to install.
The option that would give the highest quality while using the stock head unit would be to use either the MTX Re-Q bass converter or the JL bass converter. However, the Re-Q is about $150, and the JL is around $225...that being said, I would still go with the LC-2.