Intuition and imagination help in assigning crystals to these values. Aquamarine is logical for the Water area, and amethyst and lapis seem to me to signify Air. Other stones call for more subtle and subjective interpretations. Rose quartz, being related to the heart and to emotions, might belong in the Water area. Perhaps, though, the color pink can be interpreted as soft or quiet fire.
Green stones are especially interesting in terms of placement.
I find that what works best when I am using this method of arrangement is to experiment, moving the less obviously-related stones around until it feels that they are in the right place. In using this method you treat the area which will be the surface for your fountain as if it were a room or house. Please see the article on feng shui for more details. In feng shui what is placed in the center of the room or house is the most important element. I noted in the description of the chakra method that I like to put a quartz crystal or sphere in the center.