Because much of organ music consist of polyphonic works with several independent melodies, it is important for the organist to be able to hear and play each voice independently.
If you focus on emphasizing different voices, your playing will become very clear and much more interesting to the listeners.
By hearing each voice independently you will let your audience appreciate the structure and the thematic material on a higher degree.
However, if you want to achieve such level in organ playing, you must know the correct way of practicing polyphonic compositions.
Practice solo voice in polyphonic works.
If you take an unfamiliar organ work and try to play it as written right from the beginning, there is a high chance of missing many important details, such as articulation and phrasing.
In addition, you might make many mistakes.
However, if you truly want to master a polyphonic piece and play each line independently, I suggest you practice solo voices first.
Practicing this way might save you a lot of energy and you will avoid frustration.
In fact, you will master each line separately and know how the piece is put together.
This way you will build a solid foundation for your further practice.
Make sure your fingering, pedaling, rhythms, articulation, phrasing and ornaments are precise in each voice.
Practice two-voice and three-voice combinations.
After you master each voice part separately and are able to play them at least three times correctly in a row, work on two-voice and three-voice combinations.
This step will be more difficult to master, so take a slow and comfortable tempo in which you can play without mistakes.
The most challenging combination will be the one which requires to play the left hand and pedal part together.
Coordinate the releases.
After you can play three voices together in a polyphonic composition, make sure your releases are precise.
This means that you have to treat each voice separately with correct articulation.
Often suspensions and syncopations in one voice must be played using a different articulation from other voices.
Work repeatedly in fragments.
The best way to practice either each voice or various voice combinations is in smaller episodes or fragments.
This way you can either prevent making mistakes or to correct them immediately.
Therefore, I suggest you avoid playing long episodes or the entire work, at least in the beginning stages of your practice.
Note that you must try to notice and execute such details, as articulation, ornaments, fingering, pedaling and phrasing correctly.
This way your voices will sound very precise and independent.