Everyone wants to have the main method of practice so that it could be applied to various pieces. I think, the secret to this is simple: analyze the piece and practice in smaller units.
I will give one example here. Let us imagine that we take a new and unfamiliar composition. How do we start to practice it? I think, it is a good idea to get familiar with the piece and sight-read it in a slow tempo. As we play it through, we have to try to notice a few things here. First, look at the form or the structure of the piece. How the piece is put together? Look especially for repetitions because they help us to perceive the form of the composition.
Once we know the form of the piece, next step would be to analyze the tonal structure of it. Here try to look for cadences and answer the question what keys or tonalities are used in the piece.
Once we know the tonal plan, try to think how the new keys are related to the starting key. For example, if the starting or the home key is C Major and the new key would be G Major that means that the relationship between the home key and the new key is a 5th scale degree or the Dominant.
Now, if you have analyzed the piece and know the form and tonal structure of it, you can start practicing the music. Try to remember how many mistakes did you make when you first played it. If the entire piece was too difficult and we made more than 3 mistakes, then we have to practice in smaller units.
It could be a fragment of 1 line, or 1-4 measures. Sometimes even that is too much and we are still making too many mistakes. In this case, we could play each voice separately of that fragment only quite slowly so that we avoid making mistakes. Later, play 2 voices combined. The next step would be combination of 3 voices. And only then we could attempt playing all parts together.
Of course, later we have to play in larger units as well (1 line, 2 lines, 4 lines, 1 page, 2 pages etc.). If we practice smaller fragments first, this will become natural and easy. In other words, we will be ready to play a larger episode.
By practicing this way, you can master any organ composition.
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.