There will never be a shortage of people telling you that something won't work, but there is always a shortage of people doing things. Cloning in cubes is tough! Yes, soak cubes. Yes, there should be water in the tray! When you press on a cube it should gush with water. The cube is sucking water up and the clone is sucking water out of the cube and up into the plant. The plant is also 'eating' off of the humidity in the dome, so keep it wet brotha!
In my experience, the cut is not as important as the strain's 'clonability' If you found a good thread on cloning...or if you read the instructions that came with the cloner/ on the clonex...then you probably did it correctly.
I'd bet they are standing up and look fine today, but I'd like to see a photo
In my opinion, get away from the cubes and buy a clone king, ez cloner, daisy cloner, or build something similar. You WILL have huge root balls in 7-10 days with an aeroponic cloner and you will kick yourself for not having done it sooner.