Sorry, I don't remember exacly where I read it, but I remember reading that I'm supposed to sit back as if sitting in a chair.
The box is supposed to help get your body used to good form squats, and is more challenging that regular back sqauts (as far as weight is concerned).
It has made me used to sitting back as far as I can, and I truly believe that it has improved my back squat form.
I think the stop at the bottom takes away some of the stretch reflex, making you work that much more to get it up.
I've been using box squats on my ME squat/dead day, and have only ever done them by working up to my 3RM, gradually increasing weight within about 8 sets.