you'll definatly end up with much better sound. Leaving the stock deck is a VERY good choice, you'd be crazy to take it out, it just fits so nicely in the dash. Maybe someday down the road when you want to or can sink a little more money into the stereo, get a 4 channel amp for the cabin speakers and and get a nice audiocontrol piece to control everything.
Sony amps and subs arent all that bad... its just their decks that really suck.