Hey Billy

You're welcome, not sure how much help I can be on this subject.

I have thought about "upside down systems", as far as I know, the only way you can do it this way, would be with the use of a sump tank, however this still leaves you with the matter of having a tank lower than the grow bed (at least not with fish in it though).

I'm not sure if that is a possibility for you, but I think that would be your easiest bet, while maintaining an ebb and flow system.

I really don't know much about sumps or setups that involve them, so I can't really give you much more advice on them sorry, just know that they can be used to carry water from a grow bed to a higher fish tank.

On the topic of dividing up the grow beds, I would suggest still using one grow bed, as its said that the bigger the setup the more stable it will be, and then just sectioning the grow bed with some kind of guard with the same idea as your gravel guard (allowing water through but not gravel).

To help you calculate your volume you can use this method: Length x Width X Height divided by 231 for gallons or 1,000 for liters

So for your proposed grow bed: calculated in inches (roughly)
At 6 inches height: 360 x 360 x 6 / 231 = 3366.23377 gallons (lets say 3367)
At 8 inches height: 360 x 360 x 8 / 231 = 4488.31169 gallons (lets say 4489)
At 12 inches height: 360 x 360 x 12 / 231 = 6732.46753 gallons (lets say 6733)

I'm not sure about other media, but if memory serves hydroton displaces about 50% of the water in the grow tank, so only half the volume in that grow bed will actually be water.

This makes the water requirements for 6 inches is 1683.5 gallons, 8 inches 2244.5 gallons and 12 inches 3366.5 gallons.

If you could find media that displaces more water you might be able to bring you water needs down to something you might be able to use an IBC tote for.

I think that about answers all the questions I have answers for, that said, do please research the info I have given you as I am no professional... yet

Hope this was helpful.