Okay, so I have asked a similar question. I have a substrate base of approx 3". I ended up putting the substrate (marine sand, crushed coral and puka shells) in prior to the rock structure. I can get the rocks most of the way to the bottom, but I still have a small amount of sand between them and the bottom glass. Huge problem? The base rocks I am leaving a couple of inches from the glass, the rest will rest against the glass.