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A simple system like that can work..
I am relatively new to AP, but long on with aquariums and fish breeding ..
I have a kinda similar-to-yours system working, in the form of a small Koi Pond.. ( volume similar to larger aquarium)
In it, there are 10 fingerlings.. The sump pump goes to a canister BioFilter.. the filter feeds two 100mm flooded tubes that end at a waterfall back to the pond..
I would expect the cloudiness is from the clay balls, as could be the initial Ph spike..
On my main AP system, I use Agricultural Fabric Tubes over the GB drains, and they have to be changed every few days.. that red dust just keeps coming, despite the balls being very old..
That system is a flood and drain, and I suspect that such dust comes from the relatively continuous movement as many balls float via entrapped air..
I understand that the critical thing with full flood systems, is lots of oxygen,( as it is for the whole outfit.)
I have strawberries and lettuce growing in the tubes, back at the Koi Pond..
the strawberries ARE struggling as they really don't have enough sunlight, as it is all under a cream opaque polycarb roof..
I hope that the Lettuce will do better..
Back to your plans, if you want to persist, then I would think you could have a stand-pipe at the drain end, allowing water to overflow back to the aquarium ..
The likely most important issue is to get water flowing through ALL the bed.. 100%... so that there are no dead areas that can result in anaerobic patches.
The best thing about flood and full drain, is that it naturally sucks air back into the bed.. reducing so many problems with stagnant patches.. that I understand can readily happen within a root-ball....
Your problem is that the aquarium may not have the capacity for the ebb and flow of flood-n-drain, but this could be done via an external sump... but... this might mean two pumps.
. try to persist with what you have... I think..You have to build a system which CANNOT. owerflow under ANY fault condition..
If you want to try an auto siphon and Flood-n-Drain, you can calculate the rise and fall of the aquarium by the GB needing about 30% of the clay ball volume... ie. 30Ltr of clay will need 10L of aquarium rise and fall..
With the water entering the flooded bed... that could be at the bottom of the trough.. if you can get your hands on some Agg-Fab, you could make a filter for the pump inlet, and this might help with the dust etc..
If you can tollerate the rise and fall from a flood and drain, then it does not likely matter where you fill from..
Eg.. fill and drain at the same end.
The NOISE from fill and drain may be an issue inside the house, but that can be seriously reduced.. easily..
One issue that you may encounter, is LACK of nutrients from a small system...
My main AP system does not yet have fish and with artificially added nutrient, I can find that everything quickly goes to ZERO...
Have fun...
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