Practice repeatedly in fragments. This advice is very important. Whenever you play a challenging pedal line and make a mistake, try to resist the temptation of going all the way through the composition without stopping. Instead, force yourself to pay attention to details and work in smaller fragments. This is a great way to get used to the pedal board and stop looking at the feet. Practice smaller units, correct your mistakes, and make your pedal playing automatic.
Do not lift your feet off the pedal board. As you practice your fragments of pedal lines, make sure that your feet stays in contact with the pedals at all times. When you have to move your feet to the next position, slide them while slightly touching the pedals with the toes. This way of playing is like reading books by touching the pages written in Braille language with the fingertips for the blind people. They can feel the shapes of the special signs which then convert to words in their minds. By the way, there are many blind organists who manage to play the organ successfully because they feel the keyboards. The same applies in pedal playing – feel the pedal board and you will know the right position of particular notes.
Stay close to sharp keys when playing naturals and play on the edge of sharp keys. When you play the pedals and stay in contact with the pedal board you can try another technique which will help to make your playing very precise without the need of looking at your feet. If you need to press a natural key, stay close to the sharps. In fact, you can almost touch the sharp keys when you play the naturals. When you play the sharp keys, do not go too deep with your toes, just place your feet on the edge of the keys. This way it will be easier to orient yourself on the pedal board and gradually the need of looking at your feet will diminish.
I understand that it may seem like a tiresome way of practicing but I can assure you from personal experience that it is well worth the effort. Just keep your mind focused on your goal and in a few months you will start noticing some tremendous changes in your pedal technique.
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.