Bypass the amp, you will thank yourself later... You can run wires direct to the old harness on the OUTPUT side of the factory amp, just need to get a schematic for the wires, or run new wires to an aftermarket amp and amp your speakers, which will kill them if they are stock not long after you do that.
The factory wires from the Radio to the factory amp are like 20ga. and very very small. Just about worthless, and if your installing an aftermarket head unit, then you cant use the factory amp.
I just cut the old harness off of my old F150, the factory sound was GARBAGE, and wired my new radio direct, the previous owner hacked it up bad, I just had to fix it all, correctly.
I've even gotten rid of the whole MACH 460 in my mustang, it too was junk. "premium" sound options are total crap, and only make it harder to get around them. The MACH system was basically a MONO, and not even stereo.
The amp is located under the dash, above your right leg, more towards the center of the truck. Its not hard to get to, and is usually silver/metal colored, and will say AMPLIFIER on it.
It will take some time, and if you can get a bypass harness, then do that, but by all means, DO NOT use the factory amp, its not worth it, the aftermarket head unit will have a much better amp in it for the speakers.