I started mine with the water just below touching the bottom of the netpot, and the splashing from the aeration would act almost like a drip setup keeping the balls slightly wet. As the roots began to develop and show outside the pot, I let the water level drop until it was about 3" below the pot bottom during most of the grow.
It won't take too long for the roots to grow through the balls and be sticking outside the pot..maybe 10 days..and soon you'll have a giant network of roots filling the reservoir. As long as the developing roots can get enough moisture to sustain the plant it'll be fine, you're not trying to deliver a bunch nutes at that point and they are getting plenty of oxygen, which is what you want. The huge amount of O2 they get in a bubbler/DWC set from the aeration is the primary reason these systems works so well in the first place. Just make sure the aeration is splashing a little onto the medium in the beginning.