The two harnesses will plug into the two plugs coming out the back of your amp, bypassing it, which is what you want to do. The amp is located behing the ashtray, more or less. The two plugs come out the bottom. You can just leave the amp in if you want, no real reason to take it out. Just follow that one plug out of the headunit, and it leads to the amp. I just changed out my headunit and front speakers yesterday and today, and I'm pretty sure how it was.
1997 4runner Limited-chrome factory rims-silverstars-32"s-crooked brush guard-rear guards-vent shades- footwell lights-airelbow-amsoil-12" sub-Hella 500s hooked up but somehow F'd up-99 console-1.5" cornfeds-glow gauges-blue led dash-satoshi-Surco roof basket-now without running board=+15 hp