Well, the roots don't have to be 100% submersed in the water. It's okay if a little bit of it is above the water, however. The more roots exposed to the water, the easier it will be for those roots to absorb the nutrients in the water. You will need to blow many bubbles to the roots tho to keep them oxygenated.
Have you already started to germinate your seeds or are you in the process of designing your setup? I am making a similar system and a link to it is in my signature. Might be interesting to check it out. Maybe you will get ideas. I am still new to this style of growing myself but I have successfully grown in soil before.