hydroton works the best, after you rinse them clean of course.
i wouldn't suggest rocks from out side or anything that could add mineral and impurities into you water
both hydroton and rockwool cubes are designed to "give" with the root as it grows, many other gravels would be to heavy I think as well as very dirty.
in ebb and flow they will get submerged but then it drains down to a certain level about 5 in.
usually water only comes about 2 in up the bottom of your pots, or you root will only dangle into the water like a bubbler, or your roots are never submerged but misted in an aero garden.
many options for growing plants, read the grow faq "intensly and search all the groww journals before cunstruction" you will learn the best way for you and your space without making costly mistakes.
my 2 cents