I'm just gonna say what I know here.
You do not need to retain the factory amp to have a working audio system. What we did, and what I recommend is installing a small aftermarket amplifier in the trunk, preferably a 4 or 5ch amp, using a 4ch we hooked up the front speakers to the front 2 channels on the amplifier and used the other two channels on the amp for the oem subwoofer. To power the rear speakers we ran speaker wire from the head unit speaker out puts to the factory amp and tapped in to re-use the oem speaker wires. This worked well and sounded pretty good.
What might work better would be using a 5 channel amp so you can power all 4 speakers with the amplifier and the subwoofer.
To figure out which speakers are which on the factory amplifier, unplug the two plugs on the amp in the trunk and use a 9v battery to "pop" test the speakers, basically attach two leads to the 9v and touch two wires in the harness at a time and when you get the + and - of one speaker, it will "pop" then label those wires until you have all your speakers. Then connect those to the aftermarket amps speaker outputs. if you do not want to cut the wires from the oem amplifier, I have the plugs that fit at the store here.
I work at Brian Reimer Audio on St. Marys, come in for some good deals, ask for Colin.
My Motto: Love thy neighbors sick nasty whip like u love thy selves dirt nasty swag machine!
Dont mod your cars kids. its not worth it.