Im looking for a book about a girl with a magic eye on an air ship to catch magic only she can see

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...