Hellllllllllllllllllllpp fixing hole in roof

I would cut back the rubber roof (you can patch the cuts with Eternabond later) and investigate just how bad things are. Likely your going to have to replace some plywood and maybe some underlying bracing. There are plenty of threads/youtubes on people who have repaired similar problems with their RV's. When you open it up take some pictures and post - should be more than a few people here who can tell you how to proceed once they get better info on what the damage is.