im my findings playing with stuff like this is smooth surface doesn't stick to smooth surface unless air can be pressed from between it (super or any glue) but it you ruff up the surfaces and then use your glue or epoxy then you may just achieve your desired bond.....I just played with epoxy underwater with some rocks in my new 120 setup. I only bonded one rock to another but I learned a few things. First S-t-r-e-t-c-h is right epoxy wont bond to the smooth surface of glass or the black part of an over flow box (tried it)....but if you need to epoxy rock to rock you cant go wrong with epoxy putty, quick cure, cures under water, and sets fast ready for fill of the tank in no time.
Are you going to do a glass bottom as asked before, or fill it with substrate around said glued rocks?...are you trying to bond rock to glass (I dont even think super glue will work for that)?