I believe that Paul Anderson used a progressively increasing range of motion, he would gradually set the pins lower each workout and then eventually just squat the weight. I have heard of people injuring their backs with Anderson squats because it is very awkward to set yourself up under the bar in a low position. There is another similar exercise, usually called "pin squat" where you set the safety pins where the bar will be at the bottom of your squat or sticking point but you perform the squats top-down like normal, just stopping on the pins to break the stretch reflex. If you set the pins high it will allow you to handle more weight than normal, with the pins in the bottom it will increase your strength out of the hole.
If you are looking for an overload exercise you could try reverse band squats. I have heard of some raw lifters using knee wraps as an overload but personally I hate them, they also shift more of the weight to your hips so the movement pattern is slightly different. I think the main reason that Anderson squats never became too popular is because there is a high risk of injury.