How do you bypass the stock amp?

I'm assuming that you are talking about using an aftermarket head unit. If so it is almost your best bet to run new wires instead of trying to tap into the crappy factory ones.

If you are using the stock head unit and want to use an after market amp in conjunction with the stock then all you have to do is tap into some RCA cables into the 5 pin DIN that goes to the factory AMP. I'm not for sure which wires are which except for all 4+ share a common ground (the black wire in the bundle).

Yeah just putting in a different head unit. What wires do I change out?

Honestly, nothing wrong with the factory wiring. Have ran stereo systems in excess of 3000 watts through factory wiring. If you are hooking up an aftermarket radio, you dont have to bypass the factory amp, you can simply turn it on and still retain that speakers, the amp turn on wire, which is usually blue with a white stripe from the aftermarket radio, you can connect it to the adapter harness' blue/white. If you unplug the amp, you should still be able to have sound, just not from the dash tweeters.

Have a great day!!