The book starts out with a girl with magic eye on a flying ship to catch magic sand only she can see. She has no memory of how she grew up. At the start of the journey a man destroys the ship, but safes her. During the book(s) it is reveled that the man and she herself are basically here to destroy humanity because humanity threatens magic. Instead she decides to destroy all magic herself at the end of the last book.
Edit:
Humanity retreated to safe parts of the world where magic isn't as strong. I think these parts are mostly cities and used completely by humans. Because the magic found in the wild and the land itself is deadly to humans, they can only traverse it using flying ships. Further they use these ships to gather magic gathered in storms to power their machinery. There is also a part where she travels with the demon boy through the wilderness which is super magical and beautiful.
This sounds like a good book to me, really hope you find it again as I know what it's like to vaguely remember some show, movie, or book from years ago and not know what it was called or how to find it again.
Definitely would love to read it if you find it, that sounds like a great book.