I have a Pioneer 940BT in my 2003 Boxster which I can definitely recommend. I have the head unit running the dash and rear speakers and an Alpine 2 channel amp (sitting where the Porsche one used to be) running the 2 subs in the doors. The Porsche subs are surprisingly good with the Alpine, I would definitely get rear speakers first if you dont have any.
Pelican Technical Article: Boxster Rear Speaker Installation