i would start by getting a headunit first. i suggest this one, its the newer version of the one i have and the price they are asking is great, cheaper than ebay.
Pioneer DEH-P6000UB CD receiver at Crutchfield.com
next move onto speakers, i suggest infinity kappa series speakers, you can find a good deal on ebay.
then i would worry about subs. i run a single 10" audiobahn immortal sub with a MA audio amp. im not big on the RF subs. to save space go with a single high end sub and amp. my sub can put out twice the sound that 2 RF 12's could.
take your time on building your system, don't just go out and spend $400 right out of the bat. for $300 you could get the headunit above and a set of infinity kappa speakers from ebay. then start to save up for a sub and amp. one important thing you must know is that sony is all crap. and when you start looking at amps, you get what you pay for.