If the sub is being overdriven (i.e. it's too loud), then it's normal for it to clip.

Have you calibrated your system with an SPL meter (available at Radio Shack)? I highly recommend doing it, as it will ensure that all your levels are at the correct levels relative to each other. It's very tempting to crank the level on the subwoofer, but it often leads to distorted/bloated bass.

If your sub doesn't crank out enough bass for you, then you may need to trade it in for something more powerful.