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]
Sky Uppercut hits like this ^. The Pokemon using it also jump to hit it easier.
It depends on if the fighting Pokemon has the ability no guard with that ability can hit you no matter what