Play with the inside of your feet and point your knees inward. Very often organists who struggle with their pedal technique place their feet in such a way that the pedals are depressed by the outside of the feet. Such habit is especially common among men. This is because men are normally larger than women and they have different sitting habits. Usually when men sit, they do not keep their knees together.
If you sit this way on the organ bench, this simply means, you will depress the pedals with the outside of the feet. However, the precision in pedal playing can be attained if you play with the inside of your feet. So this means, that even men have to try to keep the knees together or at least point their knees inward. Therefore, try to depress the pedals with the inside portion of your feet or with the big toes. If you play this way, gradually your technique will become much more precise, you will get used to the pedal board faster and will not need to look at your feet.
Do not use force. It is not uncommon for organists with previous piano experience to use excess power in their playing. They transfer their background from piano to the organ and press the keys in the same manner. On the piano, dynamics can be achieved by using more or less power but on the organ this method is useless because the keyboard does not react to the applied force.
We can see the same situation in pedal playing when organists depress the pedals with so much energy that there are unnecessary sounds. Such playing can even damage the pedal action. Is you use too much force when playing with your feet, you might feel some strain and tension in your legs and ankles which might lead to mistakes. So, if you want your pedal technique to become very precise, play the pedals mezzo piano. In other words, use only the amount of energy which is needed to depress the pedals and not more.
If you want to achieve the level when you will feel and know your pedal board very well, focus on the organ score, point your knees inward, play with the inside portion of your feet, and do not use unnecessary power.
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.