I recommend getting a 4 channel amplifier, run the splits off two channels, bridge the other two channels for the subwoofer, and run the 6x9's off the head-unit. You want good sound coming from the front stage. Or if you want, get a monoblock for the subwoofer, a 4 channel amp to run the splits and 6x9's, and get an RCA 1-into-2 splitter so you'd have 3 RCA out's in total.
My car audio:
CD tuner: Alpine CDA-9884E with Ipod interface
Front speakers: Alpine Type R SPR-17S 6.5 component speakers, powered by a avant-garde 23dxi 2 channel amplifier - 2x51 watt RMS
Rear speakers: pioneer coaxials connected to tuner
Subwoofer: Alpine Type R SWR-1222D 12" 2 ohm dual voice coil 500 watts RMS powered by a response precision 2x150 watts RMS 2 channel amp bridged to 500 watts RMS @ 4 ohms