You put hydroton in the net pots only. I would cut the rockwool cubes in half roughly. I actually just put my rooted cuttings directly in the hydroton. You want most of your pot to be clay pellets. That would give you rockwool for your other seedlings. You do not want the water to touch the pots, except when the pump is on, which should raise the level enough so that the bottom half of the net pot gets wet. Your roots will be dangling in air to get the maximum oxygen possible, but a few inches of the bottom of the roots should be in water in case your electricity goes out or something. You need to time the pump on times carefully, or make sure there is an overflow. In fact, just make sure there is an overflow. You want as little nutrients as possible to get to the roots believe it or not. In other words you want maximum pump off time. Look around and see what people are doing for ebb and flow, but maybe something like 2 minutes on and 1 hour off.

GH nutrients are good. I use Fox Farm stuff, but both are good. Correct, no nutrients for the first 2 or 3 weeks, depending on how hearty they look.

I would keep an air stone in each bucket, or a big circulation and aeration pump in the reservoir.