First, your repertoire should be within your technical reach. This means that if the organ piece is too difficult for you at the moment then you will face a higher probability of frustration. Consequently, you might even quit practicing altogether so the piece has to be not too difficult.
The second thing to consider is how you practice. Your practice has to be repetitive, slow, persistent and regular. Let's consider each term in detail.
Your practice has to be repetitive in a way that you should practice your fragments or episodes over and over again. This will help you to make your playing very fluent and consequently you will avoid making mistakes. Also you will correct any mistakes you make along the way because you will be repeating your fragment many times.
Second, your practice has to be slow. Even though the concert speed of your piece is fast, try to pick a very slow practice tempo. In other words, your practice tempo has to be so slow that you would avoid making mistakes. This usually means that you should be playing about 50% slower than the concert tempo is.
Third, your practice has to be persistent. This means that whenever you feel that you are making a mistake you have to go back to the beginning of the fragment and correct it at least three times in a row (usually more, because three times is just a minimum number of repetitions).
Finally, your practice has to be regular. It's no good if you just practice once or twice a week and skip two or three or more days without even touching an organ. The best way to practice efficiently is to practice regularly and this is one of the most common mistakes I see beginner organists make.
They practice sporadically once or twice a week while in reality they should be practicing every single day even for as little as 30 minutes. You don't need to practice for many hours a day but only 30 minutes might be enough so try not to skip your practice time.
Apply these tips in your practice and with time you should be able to practice efficiently on your instrument and learn pieces very fast and easily.