I would point out that everyone who has ever learned to ski well knows that Mr. Hoggs opinion of how the CPG functions is incorrect. We program our CPG with our conscious mind. After enough massed practice, it will perform the practiced movements on its own. And even after this point is reached, those "unconscious" movements can still be reprogrammed into the CPG by the conscious mind. In the same way, one can modify one's pedaling technique, and in fact it will not break down under stress. Yes, it will change under stress because it has to, but the manner of this change can also be programmed in by mass practice. The secret of champions is that they pay attention. always, to everything.
It's all about skills. This is the best video I've seen about this subject:
Pedaling Efficiency.wmv - YouTube
Answering the OP specifically, IME the most comfortable and efficient fit will have your foot flat at the bottom of the stroke. One still has to find the amount of leg extension which will produce the most power with that flat foot. This is where a pro fit with a power meter and/or lots of experience comes in.
IME the best way to develop a good pedal stroke is to spend a lot of time on the rollers, concentrating on making a steady hummm. Engineering-wise, you want the sum of the moments on the bottom bracket to vary as little as possible during ordinary pedaling. Which, as Mr. Hogg points out, does not mean pulling up forcefully on the backstroke. Also, as Mr. Hogg points out, the psoas are weak, ineffectual, and don't fire at the right time on most people. Contrary to what he asserts, I've found that one-legged pedaling on my rollers is the most effective method of getting all one's leg muscles to fire correctly and at the right instant. Lots of it. I do hours of it every year. OLP drills allow one to concentrate on one leg at a time, getting the motion just right without the interference of the other leg. I just did 7 X 2' (each leg) one legged intervals on my rollers this evening. It's my favorite Tuesday recovery technique after a brutal Sunday ride. It's good core work.
A simple way to get started on a good pedal stroke is to concentrate on pedaling with one's shoe heel cups.