Most of the hours I've spent working on my car can have been devoted to my stereo system.  Within an hour of getting the car home from the dealership I'd already ripped out the stock headunit.  I've taken the car apart a few times to fully eliminate any engine noise.  Spending the extra money on shielded twisted pair RCA cables finally fixed my problem.  One of the maiu goals for my stereo was to still have a considerable amount of storage space.  My original ported box worked fine until I went on a weeks vacation and had to put most of my stuff in the backseat.  The setup I have now is lighter and provides a lot more space, plus it looks a lot nicer.
 

The dash and seats were the only things I didn't have to take out to run the wires.

This is what the old setup in my trunk looked like.

    Installing the CD player was different in the Civic than other vehicles I've done installs on.  In order to keep the dome light and keyless entry working, the stock headunit had to be retained and powered.  Doing this meant purchasing both a wiring harness to plug into the stock harness and a harness to plug into the stock headunit.  To remove the stock headunit, you must take out the lower dash panels and then undo two screws at the back of the unit where it mounts to the dash frame.  To keep power to the stock headunit, wire the yellow, black, and red wires on the aftermarket harnesses together and also to the new headunit's harness, then prep the remaining wires for your new headunit.  To prevent the old unit from rattling, I wrapped it in a pillowcase and stuffed it behind the cupholders.  The new headunit just slips into the dash and you've got tunes.

    Running the wires to the trunk was simple, just take the interior apart, run the wires (keep power on the other side of the car as your signal wires) and put the interior back together.  While I had the rear deck off I replaced the stock 6x9's with 3.5's because they overpowered the front speakers.  I've also replaced the front speakers with 5.25's.  Once faded properly, the aftermarket speakers provied a dramatic improvement in soundstage and sound quality.