The hole is an option, you can do alot of methods and all work just fine..lol I have even sliced the entire rockwool cube half way and opended up the cube like a book and slipped the clone into it like a book mark then snuggley (no gaps) slipped it into the tray , the roots grew threw and held everything together.. I can tell you what you don't want to do if you like..Do not bend the stem when its a clone , it will die..You can bend the stem all you want on a bigger plant and it will just repair itself but not a bay, dead! and don't poke the clone stem out the bottom of the Cube. Or have your medium to wet you want it moist, not wet...put them under the covers and under neons make sure it is no higher temperture than 83 degrees 70 to 90 % humidity under the dome is fine but any higher number for those two things and they will cook and rot..dont ever give them fertilizer just ph adjusted water between 5.6 & 6.3 is the range.. I like it bang on 6.0ph personally..you can make a new hole with a piece of something plastic and clean and if you like pinch the wool gently in, like someone mentioned..after 7 days of you not touching them at all cause they don't need any more help from you other than what I have outlined you might have to give the rockwwol a light moistining until they have hopefully rooted succefully , between 5 to 14 days depending on genetics and conditions..I hope this helps..