The shadow cards can be used in a number of different ways. One way is of course to simply shuffle it in with all the other cards as you use them.
An alternative that I suggest is to sort the Shadow cards out into their own Shadow deck and set them aside. Only draw from this deck if you feel an indication that you wish to delve deeper into the presence and operation of a shadow in the reading. This is most easily indicated if the Shadow Guardian card is drawn. Use this extra card to shed light on the particular shadow that is at play in the reading.
Of course, sometimes a shadow is simply sensed, and so drawing from this deck whenever you feel it is appropriate is my recommendation.