Make sure that you make as many nooks and caves as possible. You want the current flowing through the formation in order to maximize the rock's filtration of the water, and to avoid dead-flow spots which can lead to algae blooms.
Use the big, heavy pieces on the bottom and the lighter pieces with interesting features on the top. This is to both provide a stable foundation of the structure, and to allow the nice features of the rock to stand out.
Most importantly, do not allow the live rock to rest on the glass. While it is acceptable (but not desirable) for the rock to touch the glass, it definately should not utilize the panels as a means of support. This also makes it easier to clean the glass, as you have room to navigate.