I own a 2003 GT with the 460 mach audio system. The easiest thing to do is install a new head unit (CD player of your choice), and run the sub outs from your unit into the factory amps for the factory installed subs in the doors and rear deck. You will then need to purchase an amp and sub ( I purchased 650 watt precision power two channel amp and a 10" atomic sub capable of max 1000 watts) This will be run off of your rear deck outputs along with a crossover.
Any professional installer will tell you due to the factory wiring of the car with the internal sub amps and high amps, this alternative will give you the best sound without totally rewiring the car. I am very pleased with the sound of mine (plenty of bass).