Keep in mind, this project purpose is to have better sound and bass while still able to use the trunk, the spare tire and everything else the way they are meant to be used. Finally, I don't have the intention of taking my car to any sound-off competition or compete against professional installers, so pardon the lack of professionalism. 

Oh yeah, and the whole system added about 100lbs. to your car.

For the amp, you need to run a power cable straight from the battery to the trunk. The size of of the cable depends on your amp power output. (I used a Rockford Fosgate kit from Best Buy with 8 gauge power wire. ($30 or $40)) Be sure to disconnect the battery before messing with the wire.

There is a existing hole on the firewall which is very hard to find. Look carefully from the inside. It's closed to the throttle connector (I made up the name). It's 2-3" in. above and 1-2" to right and covered by the insulation. Use a crew driver to poke through it so you can see it from the engine compartment. The below pic is the view of the wire entrance on the firewall. It's kind of hard to imagine ... Just stick your head to where the pedals are and look up, you'll see it.

Once you have the power wire install ... just run it along the door jam on the driver side all the way to the trunk ...( Head up: it's kindda hard to go pass the rear seat. So be prepared!).
Next, install the ground wire to the body of the car. I screwed it down at the trunk access.

Remove the trunk liner to get access to the stock amp by taking out marked screws. Don't forget to take out the jack panel and the jack as well. You also have to take out the tool container. Just pull it up hard (but carefully), it'll come off.

You'll see the factory amp located in front of the jack.
Below is the color coded wiring for the amp. from HELMS manual. (posted by Shawn S.)

Cut the output from amp to the speakers (be sure to leave enough wire length on the harness). Connect 4 speaker wire to amp outputs (these will be connected to the inputs of the aftermarket amp) and 4 speaker wires to the speaker input (these will be connected to the outputs of the aftermarket amp.). Locate the remote wire and tap into it (do not cut it since the factory amp needs it). About the connections, you can use the connectors sold at Autozone, HiLo, Radio Shack, or Home Depot or solder them. I recommend soldering but I was too lazy to do it.

For the inputs of the aftermarket amp, you have the choices of using speaker level inputs or using RCA converters (I used converters bought from Circuit City $20/each. 2 needed if you power all 4 channel and the sub. 1 if you just power the sub.) The reason I used the outputs from the factory amp but not the head
unit is because the output from the head unit is very weak ... you'll need a powerful amp to have decent output but you'll also get cleaner sound.

The rest of the project is depended on your layout/creativity. Below are what I did.
If you want to rebuild the trunk floor, I recommend MDF boards (Home Depot $6/each 2'x4') since they are sturdy and rattle resistant. If you have any question, ask. I'll try my best to answer.

Below are my finished pictures.