First of all, it is important to maintain the straight position of the upper body, face the music rack, and point your knees to the direction of the feet. However, in playing melodic lines which extend from the right side of the pedal board to the left side (or vice versa) it is not possible to perform such passages with ease and fluency without changing position. In other words, if you play on the right side of the pedal board with your both feet and have to jump suddenly downwards to the left side, you have to switch to different position.
Push-Off With the Opposite Foot When Changing Position
When suddenly changing direction and position on the pedal board, apply the following trick and you will be able to achieve the precision without pain and strain of the lower back. If you play on the right side of the pedal board and want to switch to the left side, find a suitable note in your music and push-off with your right foot. As you push-off with this foot, move your lower body in a position where your both knees are pointing in the direction of the feet (left in this case). On the contrary, push-off with the left foot, if the melodic line ascends to the right.
It is very convenient to change position on the long note of the pedal line. However, if you see only fast-moving notes in such episode, you still can achieve the same effect with correct repetitive practice. Take this fragment, and play it in a slow tempo a few times and try to change position as described above. Practice this fragment until you can play it correctly at least three times in a row.
Consult Your Physician If the Pain Persists
Note that the above trick applies only in cases when the lower back pain arises from the incorrect playing habit. However, as we all understand, lower back pain might have various different reasons. In such cases and if the pain persists, it is best to consult your physician for medical advice.
The correct technique of changing the position is discussed in detail in Organ Technique: Modern and Early by George Ritchie and George Stauffer which I highly recommend.
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.