I am also pretty fat and have had knee pain in the past. I luckily have no trouble with squats and in fact haven't had any knee pain since I started doing regular back and goblet squats. Goblet squats were my 'in' to squatting because the counterweight made it easy to get down low and push my knees outward, which I think helps a lot. I would echo what has been said already about making sure your knees track over your feet.

Not very helpful but good luck and I hope you post about how you get on!