Ok, so just last week i did my own sub and amp install. Heres how i did it to prevent any future threads about the same topic:
First of heres what i used for the install
10mm wrench for battery terminals
unfolded mettle clothes hanger
electrical tape
Wire cutters
pliers
flathead and Phillips screw driver (to unclip fender splash guard)
4 Gage amp wiring kit
Kenwood Exlon 1500 watt amp:
http://www.6ave.com/shop/product.aspx?sku=KENXR1S
And a sub/box similar to these:
http://www.6ave.com/shop/product.aspx?sku=KIC07DC122
1: theres a perfect size hole for the amp power wire to the battery just under the driver side finder, just pop off the splash guard and feel for the hood release cable and follow it to the inside of the fender. I simply tape the wire around a mettle unfolded close hanger to snake it into the cabin.
heres how it looked from under the hood after i did this

2:your going to have to remove the kicker panel because your wire is going to be coming out of that area

3:now remove the kicker panel on the drivers door, and put it in the plastic clips where the stock wiring goes

4: now remove the pillar cover and put the wire behind it. BE SURE NOT TO TOUCH THE YELLOW WIRING, its for your SRS system

5:remove the rear kicker panel and place your wire under it:

6: this part required 2 people for me at least,(SE and XLE only with rear V brace) you'll see a little spot to snake the wire into the trunk without removing the seats, remove the cover in the trunk that surrounds the center pass through and have a friend push the wire back there, it should appear and you can just grab it and pull it up. Now your power wire is in your trunk and you can put everything back together. You can ground at just about any metal in the trunk...Sence i have the SE i grounded to the Vbrace behind the back seat.
Now for the remote wire, i personally used the power outlet in the center stack, just pop that whole thing off and tap into the RED wire as shown:

you can snake that down and under the pass seat and behind the kicker panels on the passenger side as shown in the pics above.
Now for the line out converter at the JBL amp, the wires for the rear speakers are:
Rear left + blue
rear left - yellow
Right rear + green with white tracer
Right rear - Brown
All of these wires can be found at the wiring harness closest to the front of the car on the JBL amp:

Now you can run your RCA cables back to the amp on the passenger side right next to the remote cable. You now have a well hidden professional looking install.
heres how my final product looked:

I'm sure i may have left some small details out as i made this thread AFTER i did the install so if you have any questions just post here and ill answer to the best of my abilities.