I can't edit my post now so I've gotta double post.
I reread my question and I think this is really what I'm asking.
Am I getting the best of both worlds by having some parts of the roots completely submerged all the time while some roots (about 6-7 inches) are getting lots of oxygen and only occasional water? Or am i losing out on the potential of a true aero system by leaving any of the roots submerged?
Oh and
@Nutes and Nugs I tried cutting some roots on a plant once and it really fucked her up… tons of wilting. How did doing that effect yours? As for the ones without roots you could try shaving off a bit of the outer layers of the stalk.
@panhead I'd be interested to see your results. Just a little bit of aqua shield seems to completely cancel out the root rot problem and there are no other problems i can see.