I use smaller net pots (3") so my process may be a little different, but maybe it will help:
I never have the water level higher than the bottom of the net pots.. and that is only for the first couple of days. The air stones should create enough bubbles and humidity, that the hydroton stays wet. You can tell because when I lift the net pot up water drains from the hydroton.
I also top feed for the first week or so with non-PH'd water and hydroguard (not needed root inoculant) out of a bottle of water around the hydroton to try and force the roots to search for water.
After you see a root sticking out of the hydroton, lower the water level a couple inches under the net pot and you will be golden!
good luck!