Simple question to answer.

When placing the plant in the netpot, there should be a small layer of rock below the plant stem inside the netpot. This way the stem isn't exposed directly to the splashing water. The netpot should be elevated slightly ABOVE the waterline but still close enough to allow the popping bubbles on the surface of the water to splash the bottom of the netpot. The rocks in the netpot will wick up the necessary water to the plant stem, and the roots that grow will eventually crawl out of the netpot and down into the reservoir.

I recommend placing as much of the stem in the netpot as possible while leaving one layer of rock below the stem. I do not recommend allowing the stem to remain below the waterline once past the clone stage.