Here's how you go about upgrading the headunit in your BE/BH, that uses the Macintosh amplified system.
The Macintosh units do sound and perform pretty good in their own right as a factory setup, but the main reason why people upgrade them to aftermarket headunits is because they require more functionality. They want to play MP3 coded CD's, connect MP3 players easier, subwoofers, higher powered amplifiers and the like, which is really quite hard and can be expensive if you get adaptors and such for all your devices.
The process to change the headunit is the same as here: http://www.clubsub.org.nz/forum/index.php?/topic/712-upgrading-the-headunit-in-your-bebh-non-macintosh-ampd-system/
Doing this will also remove sound going to the factory "sub" 6x9, but most people would replace this with an amplified aftermarket subwoofer.
I won't go into how to hook up speakers or subs as that's quite easy. If anyone wants this info they can send me a PM. Any 6" speaker will fit into the factory speaker fittings, you'll probably just have to cut the angled backs off them if the magnets are too big.
Remove the trim on the passenger floor side to expose the wiring, and find these two plugs
Cut the two wires that are Green with White stripe and Brown with White stripe, as pictured
Cut the Pink/White wires with a little bit of length (as pictured) to allow the connection to the other wires you just cut. Remove the black cable protection to expose the wires
Connect the Pink wire to the Brown/White wire and the White wire to the Green/White wire.
Tuck the wires back in and replace the trim.
On the drivers side, repeat the same steps and find the same two plugs. Instead of the small plug having Pink & White wires they are Purple and White, and from the big plug find the Red/Yellow stripe & White/Black stripe wires (as pictured)
Connect the Red/Yellow stripe wire to the Purple wire and the White/Black stripe wire to the White wire (as pictured)
Tuck the wires back in and replace the trim.
You will now have all front & rear door speakers going.