Why not put him on the bottom "bunk"? You should be able to cope with the extra height and getting in/out as you're taller (I assume). Same works for him (lower hammock / shorter). You're out of the fall zone of night time accidents. He's also lower so that if he does fall out it's less of a drop.
Worrying about him landing on you seems unneccessary, to me. I assume you're checking everything on his kit and when it's set up (if he does that). Therefore, the likelihood of the rig failing is the same, whether he's above you or beside. Just don't see it as a real issue.
There was also a post on here a little while ago about using spreader bars setting up two hammocks side-by-side off the same two trees. TBH, there's probably loads more such threads on HF, I just haven't spotted them. Side-by-side might be a better alternative for you and your kit?
Last, I just bought some grip clips to join tarps together. Not used them yet but I got them specifically so I can create one "big tarp" out of the ones I have for when I take either or both my kids.