You're now doing the hardest part of the entire install. Having just done this a few weeks ago, I may be able to help. Here's a link to the instructions with pictures from the guy I bought my rear speaker kit from. It should answer most of your questions.
http://members.roadfly.com/a9dbl4/BOXSTER.pdf
Wrap the loose wires together with electrical tape, this makes feeding them through everything a little bit easier. Since you have a '04, the wires should feed all the way into the front trunk to install into the connector at the amp. The guy I bought my kit from would also be a good one to ask, as he has a kit for both styles (connect at the back of the radio vs. connect at the amp).
Here's his latest auction..
http://cgi.ebay.com/ebaymotors/ws/eBayISAPI.dll?ViewItem&rd=1&item=7976277374&category=42612
You're going to have to take quite a bit of the interior panels on the passenger side loose and it's still going to be a real b**ch to feed the wires along the door opening, thru the metal guard for the airbag sensor and then up inside the front kick panel and behind the dash....and if your's connects at the amp rather than the radio, you then have to feed the wires thru the firewall and over to the amp. You might do a search for the CD changer retrofit for tips on feeding the wires thru the firewall.
It took me an entire afternoon to feed the wires on mine. I feel your pain....
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