I let the roots dangle down to the bottom and get filled in around the stalk. Be carfull when you plany your clones, don't pull up on the clone once your dirt or whatever starts to layer over the roots, they will rip off the stalk real easy. Carfully hold the clone in a 16 oz cup as you pour your dirt in slowly. make sure your stalk ends up low enough to support the plant once the cup is full. I like to give the cup a gentel tap on the table to pack the soil a little before the first watering. Hole the plant wile your first water so the plants don't fall sideways. Good luck cloners are soooo awsome, check out my pics there are some good shots of my cloner.