Here's how I do it.
If they're little plants and the roots aren't out of the cup yet, I set my water just below or just touching the bottom of the cups. With most media the spitting of the water from the bubbling will keep things plenty moist. (If you have enough bubbles it will look like the water is boiling. If not, get more air and air stones.)
Once the roots hit the reservoir things take off like a rocket. Let them drink it down a little ways. Actual water level isn't critical at this point, just make sure there's enough and that the ppm and pH don't go crazy on you. So long as there's a good amount of root mass in the water, you can actually let it get pretty low. I don't recommend it, I'm just saying it won't kill the plant fast.
But you want lots of roots with access to water, since that keeps them healthy and promotes more growth. Remember though, that spitting action from the bubbles will keep a lot of roots moist above the water line. I've had the reservoir a good six inches or more below the lid and still have the underside of the lid soaking wet 24/7.