Your power wires can run under the driver side and you can run your speaker wires up through the center console. Or you can run them back up the passenger side and under the dash to the driver side.
Assuming you're using the stock speaker wires you'll only need to run them up to the rear of the head unit.
For mounting the amp under the seat, use short screws and only tighten them into the carpeting. It will hold your amp and you won't need to drill any holes in the floor. I would however advise you to drill into the floor just to make sure it doesn't move around on you.
There is much more room under the front passenger seat too. The jack is mounted under the drivers seat.
