I'm hardly an authority on this subject, but what I am trying to learn is this: Everything we do in our technique should be powered and guide from the atemi. This is not ment in such a manner that we should hit or kick uke all the time, but we should at all times during the execution of the technique be in a position where it is clear to both uke and nage that a strike could be launched. Thereby discouraging uke from carrying his attack all the way to the end, and giving nage the best possible balance, center and power.
The way I see it atemi is the art of NOT hitting the opponent while at all times being able to. Once you have connected to the ground and your body is ready to deliever the force neede for cutting or knocking down uke then relase this energy into the technique.
The hard part is to not give the impression of a being dangerous, which will easy occur if you are overdoing it.
I like to think of it as the 'Martial' part of Aikido being a 'Martial art'.
Just my point of view at my current point of development. Hope it helps.