One of the great things about the world of Hammond playing is that it's huge--so huge in fact, there's room for everyone! Whether you are a beginner or a pro, a I-IV-V blues player, or an avant-garde jazz experimentalist, there's always a way to sound good on the Hammond. That being said, please challenge yourself to explore the variety of players and styles out there--learn as much as you can.
(Personal note: I first became enamored with jazz theory when I realized that having a solid mental-theoretical foundation made learning new tunes easier, and it gave me a broader palette from which to draw ideas for soloing. It's the closest thing to a "short cut." Learn your theory!)
Note: The original hammondjazz.com website contained quite a bit of 'legit' theory as well as jazz theory, but in this, the newer revision, we're going to concentrate primarily on jazz theory. Enjoy some improved typesetting (thanks to GNU lilypond and MuseScore) that should provide you with better, printable, examples to take into the practice room. I hope you find some of this useful.
If you're just learning these scales, see if you can memorize every one, in every key. Get to the point where you can play a two-octave ascending/descending run
(at a decent tempo, say, sixteenth notes at 120bpm or more) on any pitch, on command.
Organ Practice Tips to Keep it Fresh:
As of today, we have one set of exercises available--modal scales. More are to come. If you're looking for additional material, check out Jamey Aebersold's jazzbooks.com and check out the various scale and pattern books available there.