Most organists require FINGERING AND PEDALING in the score. The amount needed will depend on the difficulty of the piece and the ability of the organist. Use the following as a guide:
Supply enough fingering and pedaling that you can play a passage the same way each time.
Some organists prefer to mark all of the fingering and pedaling needed for the entire piece prior to learning any of the notes. This approach actually becomes a meticulous “first learning” of a piece, and comes highly recommended.
For those who prefer spreading out the fingering and pedaling process over a period of time, it can be supplied section by section as the piece is learned. This has the advantage of proximity--the fingering process takes place closer in time to the more thorough learning process.
Whatever method is chosen, use pencil for marking fingering and pedaling, and do not hesitate to make changes as you discover more natural and efficient patterns.