The height of the holes in the pot sidewall is more-or-less arbitrary, but in a pot that is under about 6"-8" diameter, I found that 1"-1.5" is a good level. For larger pots, I usually make it deeper.
There isn't nothing "magic" about the holes or the water depth. A deeper reservoir holds more water, so can wick it up for a longer period of time, and shortens the distance to the top of the LECA, which can keep it moister, higher, if your RH is too low. (Semi-hydro culture does NOT substitute for adequate humidity. If your RH is low, do something to correct that.)
When you pot up a plant, make sure the roots are NOT reaching into the reservoir. They will grow there, but inserting them will lead to suffocation.
Water the plant frequently. How much water is in the reservoir is a minor point. What it's chemistry is (think about plant exudates) is a significant point. Fresher is better.
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