Hello kargren,
I'm not sure if I understand your planed setup correctly. I attached some pictures of how it seems to be described to me. Let me know if it wrong. If I understand correctly you plan to put rock at the bottom to cover the 4 inch PVC tube, then have another tube that comes up through the end cap of the 4 inch PVC tube. That tube is attached to the
pump in the lower reservoir, and comes all the way up to the dippers on top of the
growing medium (vermiculite) to water the plants.
And you plan to have some holes drilled into the side of the 4 inch PVC tube that will allow the water to drain back down into the lower reservoir. These holes will be drilled at a specific height in order to maintain some water at the bottom of the tote with the plants at all times (about 1 inch of water) Witch you plan to aerate. You plan the growing medium to be 9 to 11 inches deep (4-5 inches of gravel/rock, and 5-6 inches of vermiculite).
Basically you are wondering by having the one inch of continues water in the bottom of the tote with the plant (even if it's aerated) will keep the roots to wet/saturated for a ephedra plant. I am not familiar with ephedra plants I will need to look them up, and unfortunately I'm out of time right now but will look them up later tonight. But I would think likely not. I am also not sure how extensive there root systems get witch would be a concern in the total amount of growing medium used providing enough root space. Though I don't see anything really wrong with how I assume you have it planed, I would do it a little different that would be easier to build and maintain and still accomplish the same thing. But I don't know what materials you have available to you, and/or even if I'm picturing your planed setup correctly.