If you dont want to use up your rocks u can get a big black bag and cut holes out for plants, it will help with clean up too. i used your same exact setup once and thats what i did, u can then use a white bag on top of the black one to reflect light and heat, But the roots must be in darkness. If thats the 3x3 ebb and flow table i have the same exact one. the bags can be a b*tch sometimes and i wound up finding a lid to a container that i cut holes in for the net pots to sit in and it sat on top of the table. This is where creativity pays off. i searched for a long time and never found a lid insert for this 3x3 system.