bottles supposed to remain filled with water
 

concerning the 11 plant two litre system, are the bottles supposed to remain filled with water or once they are filled am i to turn off the pump and let the roots remain in the solution until all water is gone and then repeat process?? Must i be aware of drowning roots?

No the roots should not sit in water. Wet the roots about every 30 minutes or so and drain immediately.
That's why I like grow rocks because they hold so much oxygen it is almost impossible to over water your plants