Our son was having difficulty going to sleep. He wanted us to stay with him until he fell asleep. Then he would wake up upset we were still not there. Our doctor suggested that we set a time limit (I will lay down with you for 2 minutes) and then leave. Our doctor said that if you are in the room with a kid when they fall asleep, when they wake up during the night (we all do this and for the most part we roll over and go back to sleep) and find you not there, they panic.
I expect you have already done this, but make sure you explain it in simple terms to your children. I have found that I often underestimate my children's ability to understand and to help me problem solve. Ask your son what makes it scary, will a nightlight help?
And then be consistent with having them in their beds. These are the things that have helped us.