In my opinion, you take the MSF course to learn how to think while operating the bike. (Keep your chin up and look where you want the bike to go when turning. Also, scan ahead for trouble are some of the points that go through my head constantly while riding.)
While you are there, you are using one of their bikes and they let you beat it up pretty good
But then, on your own bike, you'll want to be more careful with it. However, after the course, I recommend you find a empty parking lot with your own bike and really practice hard braking and manuvering with it to learn it's tolerances since it's what you'll be riding all the time. At the same time, this will make you more comfortable and confident while riding it in traffic.
You'll be surprised how quickly you make progress.
I also second the suggestion of reading Proficient Motorcycling. I'm almost through the book and it is a great refresher and reference to what you'll learn in the MSF course.
Have fun!!!