The usual practice session of many organists looks like this: they take an organ piece that the like and play it from the beginning until the end several times and take another piece and do the same. So their time ends and they call it an organ practice.
However, it is far from an efficient and effective organ practice because it lacks the proper structure, direction and goal. If you just play your pieces from the beginning until the end, chances are you're not developing the skills that you need. You also are not learning your pieces to the best of your ability.
Instead, you should work on mastering each individual piece. Here's what I mean: you should be striving to make it an error-free, fluent, musically interesting, and enjoyable to listen to. This can be accomplished only if you have the proper goal for each and every of your practice sessions.
So in each individual practice session you will have to know specifically what you need to master and what kind of steps do you have to take in order to achieve that.
One of the best ways to practice your organ music is to work on individual fragments repeatedly. In order to better control your movements and avoid making mistakes, you have to choose a very slow tempo and work on perfecting separate voices or parts.
Only then you can go on practicing two-voice combinations and three-voice combinations. It would be a mistake in many cases to attempt to play the entire four-part texture right from the beginning because this kind of texture simply will be too difficult for you at the moment.
However, you should structure your practice in such a manner that you take one step after another and little by little you will succeed in reaching your goal of that particular practice session. Remember that one practice session leads to another and so on until you master the entire piece.
Think about these tips when you practice organ playing and implement these steps and techniques in your everyday structured practice. This will help you to achieve much higher level than you are currently in.