Your rack can not be too far back or too close to the tire.
If you're rack isn't far enough back, you can't carry a big box on it because your saddle will be in the way. More importantly (for most rack users), a rearward rack position will prevent your heels from hitting your panniers.
Lower is better because your bike will handle better if your load is carried lower. Another advantage, if you pick up a nail that is longer than 3/8 inches, your rack might remove the nail before it comes back around. This might prevent a flat. Most objects that cause flats do not penetrate the tube until the tire has gone around a few times. Each time you ride over the nail it goes in deeper.