welll i had mine done and alll but i seen where they put it .. it's though the wire wall on the drivers side i guess there was a lil hole there already ... and they ran it on the driver side and the rca's on the pass side soo that you dont get a humming sound ... i guess just look on your fire wall for a whole with somehting over it ....
run the power cables on the same side of the car that the battery is on. Run it along the inside of the fender and across the back of the firewall to a removable rubber grommet. Poke it through and run it under the moulding between the door and the carpeting to the back seat and into the trunk. Make sure you run your RCA cables on the opposite side of the car as your power.
note: this is not the only way to do this, it is the way i did it and there are no problems at all.
Try going without a cap first. They don't do as much as they are advertised to do. It's mostly hype. If you have good wiring and solid grounds, you should be ok. Don't forget to upgrade the ground wire from the block to the chassis with at least 4 gauge wire. Really, your big three, battery to ground, block to chassis and alternator to battery positive should all be the same size as your biggest power wire.
How are you running the wires from the cap to the amp. Do you have the power wire going to the in on the cap, then out to the amp? Then the ground from the amp out to the other side of the cap, and a wire from that side of the cap to a chassis ground?
Also, I can attest for the helpfulness of a capacitor. I've studied a decent amount of electrical engineering, and my capacitor does exactly what it is suppossed to do. You do not need one, especially with a system that draws minimal current however, with a larger system, they are very helpful.
My system hits a lot harder with a capacitor, and my lights don't lose any power.