Here's my "If I had to do it again" plan . . .
I have my rock on eggcrate, and it helped steadying up the rock as the uneven bottom of the rock settled into the eggcrate better than just on the flat glass.
However, if I had to do it again, I would take large globs of aquarium-safe epoxy and put a few on the underside of the rock. The globs would have to be large enough so they extend past a plane formed by the lowest portions of the rock (Although they could be longer than wider). Then I'd set the rock in place on the glass, the globs of epoxy would squish down a bit, and once they hardened, form "Feet" to hold the rocks . . . er, rock steady. If the rock doesn't want to naturally sit exactly how you want, you may have to support/prop them up until the epoxy hardens (not very long).