If there are speakers in the rear deck then the subwoofer amplifier will be in the trunk on the right-hand side behind the panel. It's just a standard 2-channel amplifier that outputs 28 watts RMS per channel. My guess is that they are blown. When factory speakers quit working, everyone jumps to blaming bad connectors or a broken wire somewhere in-line. The fact is it's very rare for the connectors to fail, and VERY common for the speakers to fail. It does happen, but not very often.
As far as replacing the speakers, it's very easy. The factory speakers are 6"x9" 4-ohm impedance with a power handling of 28 watts RMS per speaker. Aftermarket 6"x9" speakers fit perfectly in the factory mounting space and you don't even need speaker brackets. You might want to add in spacers to raise the speakers closer to the openings in the panel, that's up to you.
And like bbf2530, I would also highly recommend Crutchfield.com as the best place to go. They have the best customer support and help line by far.