When you transplant, do not use a potent soil like fox farm, straight out of the bag. You might kill your clone. With brands like fox farm ocean forest, you will want to add maybe 50% perlite and flush the medium with 3 gallons of water. don't worry, this stuff has PLENTY of nutes, and it has worms, so turning the soil over brings it back to life almost instantly. Or 1 cup of fresh fox farm mixed with used fox farm will reactivate it. When you harvest your plant, pull out the biggest roots, and let the rest go completely dry for a week or so. Stir it to make sure the leftover roots dried up. Now, mix with one cup of fresh fox farm and flush with a gallon of water. Presto, instant recycled soil with just as many nutes as when you first opened the bag.
So flush the soil with a few gallons of water. Plant your clone in the soil. You can bury it all the way up to the leafs if you want. This will keep your clone a little shorter and use the extra stalk for later root development. But it isnt an easy maneuver. Best to plant them like normal, with your rockwool, etc, an inch below the soil.
Cut the top off of a 2 liter bottle and sit over the plant. Now you have a humidity dome for soil. Every day, take the dome off for an hour or so to see how the plant will respond. You have to gradually move from clone to veg, best to do it under a blue CFL. The lack of humidity, the colder air, the light intensity and the nutrients in the soil could kill them. They are essentially seedlings, afterall.
Me? I don't go straight to foxfarm. I plant my clones in 5x5 pots with peat and perlite. Then, after two weeks, I transplant them to fox farm in 3 gal potting bags. I have never had to use a humidity dome for transplanting when i did it like this, and my clones always lived. Unless I fucked with them. Roots are super brittle, and if you go looking for roots, there's a great chance that you'll destroy the root simply by finding it.
Oh... but you're growing hydro? Okay, then in that case, when you pull your clones from your bubble cloner, they can go straight into the net pots. I would line the bottom with coco coir and make sure the yellow on the stem, not just the roots and rockwool, is completely covered by your medium. For those using DWC method, make sure the water level is high enough to reach the bottom 1/4 of the rockwool. As your roots grow, lower the water so that the roots are always submerged, but there is always a 1" gap between the water and the net pots. This gives about 15% of the roots straight air and ensures they don't drown. When using nutrients, start off by adding a diluted mixture, maybe 1/4. Then each feeding, bump it up to half, then the full amount. Then increase it as the weeks go according to the manufacturer.
Same applies for aero, fogging, gravity feeding, top feeding, ebb and flow, etc etc etc, with the difference being the water level.
If THAT doesnt work, I'm coming over to show you how to do it, and you'll owe me $5