Mine are just even witht the top of the triple clamp.
Adjusting them high, and were talking millimeteres here, makes the front end react much quicker. Lower in the forks, vice versa. I haven't heard of peeps lowering them, but I don't know everything.
If you ride tight woods, you might want to experiment a little with it. Just take your time and make small adjustments.
I imagine that if you adjust them high, you can increase the possiblity of head shake at speeds. Since I don't ride fast and have a damper, I have not had that problem. I also have an aftermarket triple that is much more substantial in the strenght department, so that helps as well.
Brad