ok, i may be missing what you have going here but let me explain a little and see if it helps.

I use DWC.
I have a bucket of water mixed with nutes and ph adjusted.
I have a hole cut into the bucket lid where the net pot sits.
The water level in the buket is about 1/4 inch below the bottom of the netpot.
I have 2 air stones (this is for a bucket that is 5 gallons, if you have bigger, you should have more air stones) that are bubbling 24/7.
I use hydroton as a medium, it is cheap and the best (in my opinion).
As the plant uses water, put more water back in. Keep the water level close to the net pot for a lot of reasons that you can learn about as you go.
Change the water/nutes every couple weeks.

And there you have it. That should create a great growing environment.

PS: In Deep Water Culture (DWC), the roots are always submerged in water, as long as the water is oxygenated, this is a good thing.

I hope this helps as i am getting confused now. LOL