First of all, let me explain how people who struggle with sight-reading play from the organ score. Usually they look at the left hand part most of the time and play other parts almost from memory.
This is especially true when they play pedals. Since pedals are the most difficult part to master, many have a tendency to look at the pedal board. This is not so great. Unless playing from memory, we should force ourselves to look at the organ score exclusively.
So is it really possible to play the organ while looking at the 3 parts at the same time? In order to understand the complexity of this question, we need to know how our brain works.
I have to say, that it is impossible for a human brain to process several different things simultaneously. We can pay real attention to only one thing at a time. We may think we can watch TV and eat at the same time, or drive a car and talk on the cell phone but in reality, our focus is always shifting from one task to another.
The same rule is valid in organ playing, too. When we play from a 3-stave score, we have to constantly shift our attention from the right hand to the left hand to the pedals. So it's OK for you to play and look at the left hand stave. It is only natural to look at it while playing because normally it is more difficult than the right hand part (at least for right-handed organists).
Perhaps even better is to shift our attention constantly from one part to another. For example, depending on the difficulty level of each part, you can focus on the left hand part in one measure and on the pedal part - in another. If there is a manual change in this piece, perhaps look at the part which has this change and so on.
Remember that you will most likely behave differently when sight-reading and playing a composition which you know very well. The thing is the work you are sight-reading is completely unfamiliar to you and you will need to pay attention to many details and constantly shift your focus from one part to another.
A little different story is with composition you know well. The deeper is your knowledge of this piece, the less you have to look at the score. Obviously, the piece you have already memorized does not require any looking or following the score at all.
Since every person is different, you can discover by yourself where you look while playing by selecting two pieces of your choice. One composition has to be completely new and another - already mastered (memorization is not required). Compare your behavior and eye movements while playing each work. Finally, the more you play from the scores (both new and familiar), the better you will become at reading them.
By the way, do you want to learn to play the King of Instruments - the pipe organ? If so, 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.