Assuming you mean hydroton here. I'd keep some space between the waterlevel and the bottom of rooting plug. you might have to hand water/top feed until the roots hit the "res". But the space between the water level and the plug (and later on, the net pot/root mass, depending how low you let the water go) will develop air roots.
Don't have it touching the water, an inch or two gap should be good. Hope that helps. Been a little while.