Pedalling is the most important technique to learn first on the organ. If you have good pedalling technique, you'll really be able to take advantage of the organ. After that, learn good left hand chording/comp'ing technique. That shouldn't be too difficult assuming you're already proficient on the piano.
You want to get to the point where you are running bass with your feet, playing your comp chords with your left hand (dominants, 7ths, 9ths, m7ths, m9ths, tritones, etc.) and running melody or soloing with your right. Doing this gives you so much more breadth and range of sound than the piano will give you. There's a reason there are two manuals on the organ. Use them. Shouts and backing up a preacher get really sick because of the ability to play three different parts on the organ.
First thing to do is practice tapping from C to G back and forth on the pedals. Get your feet trained on the spacing. Then, learn C to F, then some scales and so on. Do it methodically and BE PICKY. You can get a classical organ pedalling technique book that will definitely help. There are plenty of exercises in those books that will get you on the right track with using correct toe-heel technique. The major difference is that classical organ pedalling teaches you to use both feet for pedalling while most Hammond organists I've observed use the right foot solely for the expression pedal.
