Originally I wired in a 6 channel amp but I got really bad alternator whine. Eventually I found using an old 2 channel amp and connecting the front and rear speakers to the head unit got rid of it. Anyway, the headunit's amplifier is plenty loud enough and the extra power of the Alpine amp over the Porsche one really brings the door subs to life.
The sound difference with the new headunit and rear speakers is impressive. I did replace the dash speakers but that was quite a subtle improvement. You dont need to replace all the wiring etc, if there is a difference you certainly wont be able to hear it - is a car after all. A bit of sound deadening in the doors is far more worthwhile.
Cant comment on the Crutchfield wiring as I just added a couple of wires to the cars ISO connector but here's a how to on the rear speakers:
Pelican Technical Article: Installing the Boxster Rear Speaker Kit - 986 / 987