I'm not a car audio expert, but I have upgraded the system on my 2000 Boxster, so here are my thoughts based on that experience.
If it were my car, I would first wire the rear speakers to the head unit because that will be relatively inexpensive and give you a pretty good idea of how they would sound before investing in more costly options.
If you have a little more money and can invest some time in working on the car, the better option would be to use the amp. In a Boxster that comes from the factory with the door speakers, the door speakers are a low-range unit. They are not subwoofers by any stretch of the imagination, but they are not full range. It is possible that the previous owner put full-range units in the doors. It might be better for you to install sub units in the doors and run them off the sub wiring in your amp. Then you could wire the rear speakers to the rear-speaker wiring from your amp.
Unfortunately, it doesn't so like you know exactly what the previous owner did, so you might have to resort to some "trial and error" to sort this out.
Here's a guide with a lot of useful information: http://images.wikia.com/boxster/images/b/b6/Boxster_speakers_update_article.pdf
Good luck.
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2000 Arctic Silver/Black, Hard Top, On Board Computer
PNP Rear Speakers, HAES 6-Channel Amp, Avic Z140BH,
Painted Bumperettes, 2004 (OEM) Top, Homelink integrated in dash with Targa switch, 997 Shifter, Carrera Gauge Cluster with silver gauge faces, heated 997 adaptive sports seats, Litronics, silver console
Last edited by KevinH1990; 11-24-2013 at 06:52 AM.
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