When I've got the beginning and the end of a story, but not so much the middle, one thing that I find helpful is making a list of things that need to happen in order to get to the ending, free-writing little bits according to the list, and then seeing if those bits can fit into the story or help it connect up. That way, I can tell what I might need to research or study.
Don't ever be afraid to ask questions, if you have to.
I have trouble keeping track of my notes, too. I need to get out of the habit of leaving my notes in random purse pockets.