Please explain me why FF uses here as meaning of missing?
When used with a feeling or emotion, "out of you" is a slang expression meaning that the person addressed is responsible for that feeling. Consider the Cole Porter song "I Get a Kick Out of You." "Kick" means a jolt of enjoyment, so the title means roughly "I enjoy your company."
"Flying fuck" is a vulgar way to signal intensity, so "I don't give a fuck" means I don't care, and "I don't give a flying fuck" means I really don't care.
So you could say, "I really missed you," that is, "I had a really intense feeling of absence when you were gone." Which is to say "I missed the flying fuck out of you."
The FF part isn't tied to just the word "missing."
To me, this is an odd usage of FF. Typically, "I don't give a flying fuck" is used to signal that one does not care one way or another, and doesn't want to be bothered. One does not "give a damn".
I don't give a flying fuck about some punctuation conventions, though others I consider very important.
Or one can say:
Go take a flying fuck on a rolling donut!
and mean thereby that one has little patience and much contempt for the other person's actions or attitude.