I wouldn't use them at all, can't see how it would be of any benefit.
However, if you are determined to use them for whatever reason, mix them through the soil and do not place them on the bottom, as this is exactly where the roots will go and if you have them on the bottom, there will be no water or nutrients available for the roots once they get to the bottom.
Also, consider this, - the more hydroton you have, the less soil you have. The less soil you have, the less nutrition there is for you plant.
More hydroton = less soil = more fertilizing.
If you are keen for some more tips from professional breeders about growing in soil, go to the Mandala Seeds website and click on their "grow guides", where you will find a ton of information that is really helpful and backed by years of research.
Hope this helps, Organoman.