I use Vix bits so the hole is centered. I just did a similar project and I think Danny sends you two different screw sizes...one for woofer and another for tweeter.
The bit size in the Vix is 5/64 on smaller and 7/64 on larger. Theoretically the pilot should be same diameter as screw shank, but in the real world, MDF is very forgiving as long as the pilot isn't too big. You'll get a little volcano on the surface, which can be sanded off or touched with a countersink. That's part of why I like to prefit before finishing.