1. The most important voices in the score usually are soprano and the bass. This rule is very important. In most cases, the soprano is the most melodically developed voice and the bass is the foundation of harmony. If you really want to keep it simple, you could even have a two-voice arrangement of your piece and it will not sound bad.
2. There are exceptions to this rule. This can happen especially in the modern music. Another exception is when the bass is absent. But even then the lowest voice is the foundation of harmony and should be kept in your arrangement.
3. Try to keep the voice numbers constant. You can choose a certain number of parts and keep it throughout the arrangement. For example, from the orchestral score, you can have 5 voices - 2 in each hand and one in the pedals.
4. Avoid playing too many repeated notes on the organ. If you see fast-moving repeated notes in the original score, keep the top note tied. Otherwise it would not sound idiomatic to the organ.
5. Check the score that your arrangement doesn't go beyond the range of organ keyboards and pedalboard. If the original goes above or below the normal range of the organ capabilities, you can take advantage of stops with 4' or 16' levels.
6. Avoid arranging for more than 2 voices in one hand. It would be quite difficult to play more than 2 constant voices in each of your hands, so keep it simple enough for yourself to play.
7. If the bass line is too complex to play it with pedals, you can either simplify it or put it in the left hand. Very often you can adjust the bass line so it is idiomatic to the pedal technique. Alternatively, add 16' to the left hand and play the bass part with it. Your pedals can even have a break or they can carry a tune in the tenor range with a 8' solo stop.
Start using these tips today in the process of arranging for organ your favorite choral, piano, chamber, or orchestral compositions. While doing so, you will not only have lots of fun but also learn a lot about how these pieces are put together which will in turn make your compositional and music theory skills much stronger.
By the way, do you want to learn my special powerful techniques which help me to master any piece of organ music up to 10 times faster? If so, download my free Organ Practice Guide.
Or if you want to learn to improvise in the style of Bach, I suggest you check out my free 9 day mini course in Keyboard Prelude Improvisation.