This is only how I do - maybe not the "right way"
I use straight hydroton and net pots mostly. Sometimes no pots right out of clone. I like to use the pots as they help to support the plants in the medium as the get larger.
Sometimes I do not use net pots but need support strings in flower to keep those plants from flopping.
So to answer you question, I find it best to put a net pot under water, put a rooted clone in it, fill the pot with hydroton, then stick the pot in my ebb tray which is filled with hydroton. This provides plenty of support and nutrient flow around the roots. I did use rockwool cubes and netpots then put them into the hydroton until I realized I could save money on the rockwool and skip it.
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