Write in pedaling. In order to avoid confusion and accidental pedaling which leads to mistakes and unnecessary tension, I strongly advice to write in all your pedaling. Pencil in your pedaling with the signs for toes and heels (left or
right foot). If you write in your pedaling regularly in your scores, you will start to feel the predictable patterns which will help you make the right choices even without writing down your pedaling. However, pencil in the pedaling at least until you are comfortable playing with correct pedaling the Baroque compositions. For Romantic and modern organ music, it is best to write in the
pedaling in every score.
Use pedal preparation. This technique will increase your pedal playing abilities enormously. Simply prepare your feet for the next note in advance. For example, as you release the note in the pedal part, slide it instantly into position for the next note. Do not play the next note, of course, but let it rest and wait for its turn. In order to be implemented correctly, this technique must be practiced over and over.
By the way, it is a very powerful technique which makes your pedal playing automatic without the need of conscious thinking. This, of course, reduces the chances of mistakes dramatically and you will not need to look at your feet while you are playing. At first, you will find that it is hard to remember the position for the next note. In this case, write in your pedal preparation in parentheses. Later, with the advancement of your pedal technique you will start to feel the next note in advance and will not need to think about the preparation at all.
If you use my advice and write in your pedaling and practice pedal preparation regularly in your daily practice, after short few months you will begin to notice that the temptation to look down at your feet gradually lessens. This will happen because you will know your pedal board much better than before.
If you are interested in perfecting your pedal technique, an invaluable resource is Organ Technique: Modern and Early by George Ritchie and George Stauffer.
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.