I Dont really understand your question, but I think that I know what you mean. Don't downvote me if I'm wrong just flag or comment.
Do you mean "How can the fighting move Sky Uppercut hit Pokemon using fly"?
![enter image description here][1]
Sky Uppercut hits like this ^. The Pokemon using it also jump to hit it easier.
///Jofly [1]: http://newsimg.bbc.co.uk/media/images/40816000/gif/_40816398_uppercut_298_anim.gif
It depends on if the fighting Pokemon has the ability no guard with that ability can hit you no matter what