Run it through the grommet underneath the fuse box in the firewall, and down the left side of the car underneath the sills. There's an opening by the lower corner of the back seats that you can run the wire through, but you have to pull up the carpeting a ways to find it. Run the signal wires down the right side so the power wire doesn't introduce any noise into the lines.
Im puttin in a 6.1 system. the 3.5'' are going to be run off of the deck and the 6.5'' and 6x9 off of a JBL 4ch amp and a 15" Diamond D6 in a custom box run by a HiFonics 1200watt D-Class amp pushin 900watts RMS