Hi Alex,
I would suggest doing your casting in layers. Youre correct, the stones are heavy, so they are going to sink to the bottom of resin. Even by waiting for the resin to cure some before adding them doesnt guarantee that they wont sink and you may introduce bubbles that way.
For easy math, lets say you have a 6 inch cube that you want to put the stones in, and youre trying to make it look like they are floating in the center 4 inches of the cube. You will want to pour your first layer to the level that you dont want the stones to float beneath. Once that layer is in a mid cure, then you can pour your next layer(s) for stones. If youre trying to keep stones away from the edge of the cube as well, you may want to do several small layer pours rather than one big one. You will have more control on how the stones pack in there. You can then finish with one big layer on top. I hope this all makes sense!