We don’t just use box squats, as I’m more a fan of Olympic style squats to be honest. We still use them though just not as much. With regards to your question Dave Tate (Elitefts.com) advocates saying ‘1000’ whilst sitting on the box then driving up. obvioulsy then main advantage of box squatting is the way it targets the posterior chain as supposed to a regular squat.
The time spent on the box is reflective of a standard box squat, anything shorter than that and you are just using the box as a depth marker. However, you must have any athlete stay ‘tight’ during the box squat, as i have seen people in commercial gyms and other organizations just drop without control onto a box-this is a recipe for disaster.
Hope this helps.