You cannot add an external amplifier to power your factory speakers. It is possible to add an amplifier to the factory system for subs. This is accomplished by using an amplifier interface. Otherwise, you will have to replace your head-unit and install an interface to use the cd player's on-board amplifier to send a signal to the Bose amplifiers. This means that the factory amps and speakers are still used. Your other option is to install a cd player, new speakers, and re-wire the new system to bypass the factory Bose system. If you re-wire the system, then you can use external amplifiers or the on-board amplifier in the cd player. With Bose, there is no simple aftermarket solution.
A company called Soundgate (
http://www.soundgate.com) can supply you with the required interfaces.
I highly recommend a good shop to do the work. The interfaces are not cheap, but you get what you pay for.