My suggestion, get something along the lines of an Audiocontrol EQX...you can then use the high level inputs (speaker wires from the back of the factory head unit). From here you use RCA cables to the amp(s).
A good cheap solution for amps is Hifonics. I wouldnt recommend buying anything more expensive because the sound is limited by the stock head unit (which leaves much to be desired). For subs, look into Image Dynamics. You can get an ID12 for $111 on Sounddomain.com. These subs are AMAZING for the price and they do well ported, sealed, and IB. They dont require a large enclosure either so you can keep most of your trunk space.
Any other questions just PM me