You don't need rocks in the bottom, and although it probably wouldn't hurt (as long as they are not limestone) it will make changing your water an extra pain.
The water level can be wherever you want it to be. If I were to use a 5 gallon bucket I would leave at least 6" below the net cup, but that is just me. You will see when you fire it up -- water will be all over the bottom of the lid -- that is why this works so well.
Doesn't the water have to touch the net pots, why would it be 6 in below the pots then? I though the water would have to come at least half way up into the net pots?
I also gave up on airstones. Just poke holes in a piece of air tubing and wind it around. It takes a little practice to figure out how to cut the holes to make them the perfect size. I use a little screwdriver that is sharpened and just poke a hole every 1/4 - 1/2 inch or so and then wind that around the reservoir. Airstones and air line are cheap, buy a little bit of each and see what gives you the most bubbling action.
That's a good idea I got a lot of extra line laying around ill see what I an do.
Good luck,
PP