When you call a plumber for a clogged drain, his solution ain't gonna be to put a new faucet in.
Same thing here... to change the sound you want to start w/ (as Porsche calls them in the 986) the "speakers". Leave room for further expansion of course in the way of a different amp (if desired) and head unit. Truly, the speakers are crap and rival a $3 AM alarm clock radio from Dollar General... no disrespect meant to Dollar General...
If you're fine w/ the functionality but just want better sound, change the speakers and you'll be surprised at the dramatic improvements. Otherwise, there are many many options as to which way to go. What is your goal? Nav, Sat Radio, iPod/phone interface, Bluetooth, etc.? Also, it helps to know what your system currently has too (base, hi-fi w/ door woofers, rear shelf speakers, Bose)?
Start by reviewing the excellent document called Upgrading the Speakers by Andy_M on the Boxster Wiki under option 2 - Audio:
Boxster Tech
Good luck
