The following advice is based on the assumption that your organ bench is adjustable or at the optimum height for you when you can touch the pedals with your relaxed feet but the pedals would not be depressed. Of course on the lower or higher benches the story is different altogether.
I think when the feet are not playing and only resting on the pedalboard, then the heels should the resting on the pedals as well.
The movements of the feet of the organist should be economical and when there is no need to lift the feet up in the air, the heels also touch the pedals.
When you're playing the pedals with the modern legato technique, then the motion is from the ankle. This means that the heels should be touching the pedals as well.
But when you're using articulated legato technique for early music, then the motion is from the entire leg and the heels will go up in the air a little.
Try to use these two different approaches on different styles of music for the most stylistically appropriate playing.