The fader basically is not used, as in effect the headunit only drives front speakers
The rear parcel shelf aftermarket unit can be plugged into the spare socket on the rear of the headunit, and then acts as rear speakers. The bose unit is a subwoofer, so still works off the front channels.
The door speakers only handle bass notes, the ones atop the dash handle highs and mids.
On the 986 the speakers are real cr4p - paper Nokia units. The headunit is actually pretty decent quality (albeit not Nakamichi or Levinson quality). The sound pack amp is not that bad, albeit a bit lightweight in both sonic and physical terms.
The only real issue with just changing the speakers is finding a matched set, as most three way kits that include a 4" midrange tend to use 6.5" bass units which means modifying the stock door housings.
MB Quart do some reasonable quality units for not huge money, after that you're into serious stuff like Morel, Focal, DLS, Diamond or Rainbow.