A key thing that I learned to do a stoppie is to do the braking in
two steps. The initial braking is kind of soft, allowing the front suspension to
compress. Once that's taken care of, you brake with the purpose of lifting your rear wheel off the
ground, which needs to be much firmer and decisive. This will help your stoppie be
smooth. Smooth is good, as having this sudden
jerk in your motion may end up causing you to look like a
retard as you fly over the handlebars.
Another thing that is important is to have your bike straight. If you are (hypothetically) riding down Spur 40 at 55 mph with your buddy watching from his truck, and try to do a stoppie when your bike is not properly aligned you will get yourself in that "look at me, I am an awesome crazy stud with huge gonads" position, and then notice that your rear end is swaying slightly to the right, and just when that starts to worry you, your front wheel, which you are pretty much above at this moment, starts to wobble. You will the see your life flash before your eyes and let off the brake, possibly screaming like a little girl, and hopefully only wobble one more time after you land, and then finally straighten out and carry on your merry way, praising Jesus that he watches over the stupid.