What he said.
Also, I still feel bad that we haven't had the chance to meed up and address this in person..
All of this depends a bit upon how you have everything wired and mounted.. Here's the "ideal" situation.
I'm assuming it's two subs in a box, each with their own pair of wires?
Drag that sub box inside, but leave the amp in the car.
Hook the subs up to the "B" speaker set on your home stereo, (assuming it can do that.) and fire up some Nine Inch Nails.. hopefully they'll both be moving, to some extent, and equally. If your neighbors complain, the problem isn't the subs..
Now take any 'ol speaker out to the car, and hook it up to the amp. Fire up the stereo and see what you get for sound from the speaker. Hopefully, you'll only be getting bass, even if it's a full-range speaker. If it sounds "normal," you'll need crossover work. If you get nothing, it's either wired wrong, or the amp doesn't work.