I spoke briefly about chamfering the sides of my EP stones and I said I do not think that it is critical to do so.
However, if you do have something handy to use, it certainly does not hurt and it is easy and quick. Also, in my opinion, it just doesn't protect the knife, i.e. a sharp sided stone could damage the edge, but it also protects the stones. Some of my stones have developed tiny nicks along the edge that is rapidly repaired by the process of Chamfering.
If you click on the pictures you can get closer shots.....I suppose you all knew that :)
For EP sized stones, I set the Atoma plate down as shown and simply hold the stones at a 45 deg angle and run it back and forth, approx 5-10 times with gentle pressure will do the trick. Don't sweat the angle too much, as long as you are making he flat, sharp edge a little less severe.