When you say "plugged into the computer's hard drive" I assume that you simply mean plugged into the computer.
Probably the square box on the floor is a subwoofer to give better bass response, although from you description that's not entirely clear.
One would normally expect to find three speakers, two of which would be quite small and look similar, except the one would be connected to the computer and the other connected to the first. These would be the left and right stereo speakers, then a third larger one would be the sub-woofer.