The Canon indeed won't fit the 100mm lens - only certain of the L lenses - because it's got a protrusion that sticks out INTO the lens...
Interestingly enough, I just used a Kenko 2X TC with my 100mm for the first time last week on a trip to Belize. I didn't expect it to AF, but was pleasantly surprised when it did - reasonably well, in fact (provided there was enough light). Bear in mind that I was using it on a 1DsMkII, which is full frame, so I can't guarantee that it'll AF as well (or at all) on a 20D. But you'll find out pretty quick if you try it. 
If it turns out that it WON'T AF, the problem with planning to use MF is that your MF ring may not fit over the TC, meaning you may or may not actually be able to use MF (my Seacam MF ring for the 100mm will NOT work with the TC, which is larger diameter than the 100mm lens).
FWIW, here was the best shot I got with the 2XTC and 100mm (an arrow blenny):
