1. Have a goal in mind. First and foremost your have to find goal which you can focus on. It could be like a dream which keeps you going. Your goal could be a general one, like to become a good organist, or a more specific, like to master any specific piece.
However, if you play aimlessly, your chances of keeping up your practice for years to come are not high. In other words, if you play one day this, another day that - such practice will not lead you anywhere. Note that I am not talking here about sight-reading which you should also practice. Instead, I am referring to the pieces that you want to master at a deeper level.
2. Have a schedule for practice. Once you found out what your goal is, prepare a plan with specific steps and schedule for your regular practice. Remember that it is important that you practice regularly.
If you skip one day without practice, only you will notice it. Spend two days without a practice and your teacher or friends will start noticing it. As the old saying goes, practice is like boiling water - without constant heat it cools down.
Note that your practice sessions do not necessarily have to be very long. Only 30 minutes a day might be all you need to start seeing some positive results after a few short months.
3. Choose pieces according to your level of ability. Try to be realistic about your technical level when practicing organ. Although your dream might be to play something technically very challenging, like Widor's Toccata, you might not be ready for it yet.
Instead, take some shorter, slower works from the same period and master them. Think of them as a preparation for your goal which you eventually will attempt to achieve.
4. Find a mentor you can trust to push you. Although you have chances to succeed when working alone, having a good mentor, a teacher, or instructor is much more beneficial. Your mentor can tell you to practice harder, motivate you, give you a daily plan, and other valuable recommendations.
However, you must listen to your mentor and do what he or she asks you to do. There is no point of working with a mentor and doing things that contradict with mentor's teachings.
Key points to remember: find a goal, prepare a schedule for practicing, practice pieces that are not too difficult for you at the moment, find a mentor and listen to your mentor. If you follow my advice, you will have many more chances to practice for many years successfully.
You can also 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.