I'm using the same setup as you except the use of "smart pots".
I use a container like this instead.
http://www.hydroempire.com/store/product_info.php/cPath/8/products_id/420
I put about an inch layer on the bottom of the pot and then I put the rockwool right on top of the Hydroton so the roots will have somewhere to go after they pop out of the bottom of the rockwool.
I think you might not want to use the "smart pots" since they're made of cloth. In an ebb and flow table, the water needs to drain out completely. Those "smart pots" look like they'll hold onto water after the drain and this invites a mildewy smell. In fact, my 4 inch rockwool smells a little mildewy and I'm assuming because its constantly damp.