1. Check if the piece is not too difficult. Very often organists with modest technical abilities have quite ambitious goals and start playing compositions that technically are too challenging or they simply are too long. For example, such a person might like Bach's or Widor's Toccata or Prelude and Fugue on BACH by Liszt or any other difficult piece.
However, no matter how beautiful these works are, beginners have to start with more modest and shorter pieces first. For instance, if you like Bach's D minor Toccata, try several shorter preludes and fugues from the collection of 8 Little Preludes and Fugues, BWV 553-560.
Or if you eventually plan to master Widor's Toccata, why not to start with an easier piece from the French symphonic school, such as Berceuse by Vierne, pieces from L'Organiste by Franck or works from Practical Organist by Guilmant.
Instead of Prelude and Fugue on BACH by Liszt, play easier movements from Mendelssohn's sonatas, or choral preludes by Brahms. Although they are short and not as difficult, the artistic level of these works is very high.
You are probably wondering, how to know if the piece is too difficult? Try sight-reading it in a very slow tempo, and if you make mistakes in every measure, I suggest taking an easier piece first.
2. Practice in voice combinations to avoid mistakes. If the piece you are working on is of your technical level then there is one more thing you can do to make things easier. In order to avoid making mistakes, which will save you a lot of frustration, try practicing your organ piece in separate voices first.
After that work on two-voice combinations, do not rush and achieve the level when you can play them at least three times in a row correctly. Then play three voices the same way and finally, the entire four-part texture.
3. Practice in fragments to correct mistakes. If after playing according to the above point you are still making some mistakes, it is best not to play your piece all the way through. Instead, work on one small episode or fragment at a time. It could be as short as 1-2 measures or longer (1 line).
If you make a mistake, just go back to the beginning of your fragment, take a slower tempo, correct your mistake and play it at least three times in a row without any errors. Note that your fingering, pedaling, notes, rhythms and articulation must be precise.
To summarize: choose the piece which is not too complicated for you at the moment, work in voice combinations and in smaller fragments for best results. Practicing this way will lead you to success in organ playing and will help you to avoid much frustration.
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.