If you bass it's distorting, it's because you're gains are set too high and the amp is distorting, or you're send too much power to the sub and that's distorting.
Like Chaos says, soundproofing is what's needed. I prefer Dynamat Xtreme (ans Chaos has an expanding foam thing going on!), it's easy to apply and very effective, but like Chaos said, not cheap. 2 or 3 sheets should be plenty to deaden your boot sufficiently. I've got 7 in the back of my Sei, 1-3 layers in the boot and 1-2 layers on the rear quarter panels and under the rear seat. Floor and roof next!
Putting a layer of MDF on the boot floor will do nothing to the sound of 6x9s, just make sure the shelf they're mounted on is rock solid.