as with all things: practice makes perfect. i agree with the above that rolling stoppies are much easier and they are (IMO) much easier on the bikes. stopping stoppies come down hard and kill the rear of the bike. plus rolling stoppies look cooler to me. why do you think the xsba has a rolling stoppie contest?
to master a stoppie: start at about 10 mph and grab the front brake. not too hard, but just enough pressure to bring up the back. no, your first few times will suck, so prepare to be disappointed. once you can get her to come up pretty vertical, then begin your stoppie at 20 mph. it not only looks cooler, but they get a lot more attention that way.
my favorite is to begin the stoppie at about 50-60 mph and start to grab the front brake. i get it to come up in back and find the balance point and just ride it on out and then gradually let her back down. i love stoppies almost as much as wheelies, but then i'd have to change my user name.
eventually you'll learn to point and/or give the finger during stoppies.
if this is something that you think you'll do a lot, i recommend stainless front lines as they won't bleed and a bleeding line can SUCK for a stoppie.