You can leave the shaker 500 system alone which consists of the small subs in the doors powered by the factory amp. As far as interiors, go with a quality set (80-100 watts RMS) in a 6x8 inch. You can either power them off the factory radio, or get a 4 channel amp and amplify them. The 4 channel amp will make a HUGE difference for overall clarity and loudness. As far as bass goes, you can do a sub in the trunk, but would need roughly 500 watts RMS in a ported (vented) enclosure to really sound good. I install sound systems at Best Buy and recently did a 2013 mustang coupe with 4 alpine 6x8s, an alpine M500 amp (500 + RMS power output, a JL audio 4 channel (75 watts x 4 channels at 4 ohm) and a alpine 12 inch type S subwoofer (500 watts RMS power handling) in a vented enclosure. It was all fed off the factory radio. It sounded a 1000x better than the factory stuff. If you want to go even further, you can get a quality equalizer to go between the factory radio, and the inputs on the amps. This gives you complete control and very precise adjustments over the sound you will be amplifying. You would have many more parameters to fine tune your sound according to your liking. I personally went with 6 inch components (Kicker QS60.2) and fed them with a Kicker IX 4 channel amp. I also used the rockford fosgate 360.2 and fine tuned the system according to the music I listen to. You don't need to rewired everything in your car. You would need to run signal from the radio to the 4 channel amp, then the output can run right back to your factory wiring behind the radio via 9 wire (made by METRA). You would need to run signal to your subwoofer amp, then the output would go right to your sub box. You would also need a 4 gauge power wire from the battery to the 2 amps and grounds for each amp. A remote turn on wire to turn each amp on can be found at the ignition harness. Grab the accessory wire and add a 3 amp fuse. Sounds like a lot, but it will make a huge difference.