Well there's a couple of good threads in the FAQ that will give you some things to think about ...
All of the info below is true for the Roadster, but I don't know whether the Coupe is the same.
First up, it really depends what kind of system you've got already. It's apparently easier with the standard (6 speaker) system which is what I'm starting from. I'm currently just starting the process myself ... at the moment I only have half the answers ! Mine might go something like this
1) 6x9" sub woofers in the cubby holes as per Richard's thread in the FAQ
2) New 6" full range speakers in the front footwells
3) The 4" mid range rear speakers at head height behind the seats have to stay - they're apparently a bastard to change ... The 4" 'speakers' in the doors are blanks.
4) For the moment I'm going to leave the tweeters in the doors alone ...
5) I'll be taking tappings from the front and rear speakers probably into a JL Audio Cleansweep or something similar. I'm doing this to keep the stock head unit, (which has has no RCA 'Line Out's). It seems likely that the front and rear speaker signals will have been processed by a (or by multiple) crossovers ... I'm hoping that the cleansweep can compensate if required.
6) A 4 channel amp in the boot, mounted on a bulkhead board at the front of the boot. This should give it enough free air to keep itself cool, and it's fairly easy to get access to all the wires from here. Bridge two of the channels to drive the subs, and drive the footwell speakers via the other two channels.
I hope to get some photos as I go.
-- Chris