for the audio signal. What I've done is to remove the amp box connector (wires inside the box are a few inches long) and then connected the 2 audio wires to the speaker and taped up the power lines since they aren't needed. This method avoids hacking up the factory harness.
You'll need to look at the online factory electrical manual for the wiring colors - it varies by side of car, front vs rear. The amp power wires are the same color everywhere - I just don't remember the color codes.
FYI - folks also run new wires to all the speakers. It's another way to go but for a low to moderate power sound system the factory wiring is fine.