Here's how you can determine if you are sitting on the organ bench at the correct height:
Sit at the middle of the bench, relax your feet, and let them touch the pedals. The feet should be slightly touching the pedals but not depressing them. There should be no sound.
If there is some sound, you are sitting too low.
If you can't touch the pedals with the heels, you are sitting too high.
Now the problem usually is when the bench is permanently too high (because if it's too low you can simply put thick hymnals or wooden blocks under each side of the bench).
If the bench is too high (and you can't adjust it's height), then try to do one of 3 things:
1. Sit as close to the edge of the bench as possible without sliding.
2. Play using mostly toes.
3. Get organ shoes with higher heels.
Hope this helps solve the optimum organ bench height problem for you.
Am I missing something? What are other things you do when you encounter the bench which is too high? Share your ideas in the comments.