roots in the water is perfectly fine. it is going to happen sooner or later. the water from a bubble setup can only pop so high, and you can't keep lowering your res levels so the roots don't go into it...sooner or later, your bottom part of the netcup, where the roots come out, will be completely dry because the root mass will get large enough to block it from splashing that high...it will still splash mostly on the center roots, but not the ones coming out of the sides of the netpot. a good rule of thumb is 2-4 inches below the netpots. the bubbles coming up from under will be used by the roots within the water. so it won't overwater them. bubble buckets are a method of DWC. meaning deep water culture. the water is pressure pumped with oxygen, making it more aerated, and the flow keeps the water from going stagnant. if you have to, add a stronger air pump and more airstones, even if it is overkill, to be certain that there is enough oxygen being pumped in to keep your roots healthy. once you have that setup properly, you'll see the good growth rates, and there will be no need for timers...and the only work you will have to do is check the PH and change/clean the res.
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