What is easiest way to hook up subs since the 3's stereo has no outputs?

 

A speaker line-out adapter connected to the rear door speakers I believe would be the answer to your question.
Remi, wanna take this one to the next level?

 

After bringing it out of the door, what is the easiest way to run it to the trunk?

 

What Virgin1 said, though from what I've been hearing recently most installers are recommending tapping off of the front speakers as the HU rolls off the bass to the rear speakers which will make the sound suffer a bit. You can tap everything directly behind the HU and then run your cabling along the sides of the car. Just remove the scuff plates on the door sills (pull straight up) and then you can tuck the wiring behind the carpet. Make sure to run the power on one side and the signal wire on the other to avoid interference.

 

Whick color wires run from the dash to the door speakers?

 

Here's the pin out

Holding the clip upwards, and from left to right, these are the colors of the wires from the factory radio harness. "-" means negative, "+" means positive.

TOP

White/Black – left front +
Gray/Black – left front –
White/Red – right front +
Gray/Red – right front –
White/Purple – left rear +
Gray/White – left rear –
White – rear right +
Gray – rear right –

BOTTOM

Orange/Black – 12v constant
Orange/Black with silver dots – 12v illumination
Yellow with silver dots – 12v ignition
Black/Green – Chassis ground

Yellow with silver dots is the wire you would want to use to power your amp remote turn on.

 

Does it matter wheather I come off the left, or right channel?