One method to keep the stone down is to get a 1 foot length of PVC pip and drill a hole just big enough for the air pump hose on the side of one end of the pipe. Then run the hose down the pipe and pass it through the hole you made at the bottom/side of the pipe. The pipes weight will help keep it at the bottom of your res and the air stone can't pass through the hole so it stays at the bottom of the pipe. You can also attach as Stainless steel weight to the air stone with some Stainless steel wire, or a plastic zip tie or any plastic tie. Maybe you could use a plastic hunk as a weight too.

I also did set up a drip system until my roots hit the water, and I ended up running the drip on a timer, it would allow me to use more of the hydroton cause it kept more wetter:stoned:, I also put these little pieces of plastic made to cover rock wool cubes to keep the roots darker.

Good luck and happy growing.