I have a shaker 500. Tried adding an amplified sub (I didnt wanna lose space) in my trunk but it made it worse. The sub output from deck doesn't have enough juice for an extra sub even if you put a mono amp for it. May be replace the door subs (they're 8') with aftermarket ones? There's a thread somewhere that tells you exactly what's their depth since they're shallow mount.
From my experience, get a solid line out converter (if you wanna persist with factory stereo), get aftermarket speakers with good 'highs', 4 channel amp set at high pass, and 10inch subs for punchy bass. Even better: aftermarket deck (it will make day n night difference to sound output) if you have extra cash.
Bottom line: this whole setup (with deck n dash kit) is going to cost you 2k+ and labor. The ball is in your court now bro