Two of the wires are power; two are signal. Refer to the factory wiring chart to identify them (on one of the threads - search and see https://www.crossfireforum.org/forum...ad.php?t=20949)

I didn't bother removing the factory subs - left them in place. Instead ran a separate pair of leads to a powered sub. But that's using a replacement head unit so probably not much help to you.

If I was doing it with the factory head unit, I would come off the head unit before the factory amp, go into the SD Clarion card, then to the power amp you have, then to the speakers, put into enclosures and bolted to something solid (not the carpeted trim panels). That's just me.