I wonder if I can get a cheap subwoofer for that compartment from like the eddie bauer explorer and hook it up with a nice amp??

Youch, don't do it man! The sub that comes with the ltd and Eddie Bauer is a massive steaming POS - it sounds like death warmed over. It's not even a proper sub, just a crappy 6" round speaker, with either a resistor/passive crossover attached - you could likely find one at a wrecker, but I bet they would charge you a hefty sum for it!