if your sub hums it's an indication for a ground loop. Meaning your install is faulty. That or your amplifier is either on it's way out or it's not of a very high quality. Also, if you have the gain on your amp turned up it can cause this noise as well.
If one sub hums and the other doesn't i'd check the wiring on the sub that hums. Make sure you have everything wired correctly.
Do you get sound if you plug in a set of head phones to the audio out jack on the mobo?
What amp, what subs, and how do you have them wired?