First of all, we have to realize that any skill, including pedal playing, must be acquired through regular and patient practice. No matter how good you may be at the theater organ, when it comes to classical pedal playing, it is just plain too complicated in the beginning. Do not despair, however, and understand that you will have to take the same steps as you would in theater organ playing.
Majority of music composed for accompanying silent movies on theater organs requires constant registration and color changes to imitate different orchestral instruments and different moods of movie episodes. In performing such music, the organist has to change registration either by pushing pistons with the thumb or use the toe studs with the foot. Most of the time, since both hands are particularly busy, theater organists use the right foot for toe studs and leave only the left foot for pedal playing. As a result, they have a virtuoso left foot technique but underdeveloped right foot.
What this means is that whenever such organists want to study classical organ repertoire, they have to start with some easy pedal exercises in order to achieve the same ability with the right foot gradually.
Do not start practicing pedal scales from the beginning. Although pedal scales are one of the best ways to develop a perfect pedal technique at the organ, they are obviously too difficult for the beginner
organist (and for theater organist as well). Pedal scales are too advanced because you need to use toe-heel technique constantly. As this is too complicated at first, start with some easy exercises which will not involve using heels in the beginning.
Choose alternate toe exercises first. The easiest pedal exercises that theater organists could practice are alternate toe exercises. This means that they involve using left and right toes only in alternation. For
example, play ascending and descending sequences of thirds. Such exercise might look like this: C E D F E G F A G B A C etc., or C A B G A F G E F D E C D B etc. In addition, play ascending and descending lines of fourths: C F D G E A F B etc., or C G B F A E G D F C etc. Exercises in fifths are also perfect for the beginning: C G D A E B F C etc. or C F B E A D G C etc.
Play these exercises legato with alternate toes in a slow tempo. As they become easy, you can choose different exercises using heels as well. Remember, that the development of the correct pedal technique requires regular and patient practice. As everything in organ playing, both feet technique takes time to
master but it is well worth the effort because the whole new dimension of organ music will open up in front of you.
An invaluable resource for pedal exercises is Organ Technique: Modern and Early by George Ritchie and George Stauffer which I highly recommend.
By the way, do you want to learn to play the King of Instruments - the pipe organ? If so, download my FREE video guide: "How to Master Any Organ Composition" in which I will show you my EXACT steps, techniques, and methods that I use to practice, learn and master any piece of organ music.