i totally remove the carpet - that means all seats, center console, side trim, etc. then i can easily route the wire to not interfere factory screws/clips and i can also take the opportunity to run RCA's and speaker wire, etc. an assload more time, but i don't just cram wire in the sill either. worth it if you are running all of the other wire also.
in fact, my carpet is out of my car right now and has been for a week. i'm re-running all of the speaker wire (8 channels to the front) and removing other cables i don't use anymore.