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As KenF said, Standard Manuscript Format is probably the way to go. Though, it also depends on the site where you upload the story. Basically, it just needs to be reader friendly. SMF is simply the standard used for submissions to magazines and book publishers.
Regarding identification as you as the author and a confidentiality notice, I really don't think you need to bother though. That is, if either of the two following assumptions are true.
1) The story is a piece of fan-fic (since you're publishing it at fanfiction.com). Then you won't be able to sell it, so why would there be any dispute over who wrote it?
2) I have never used fanfiction.com, but I would assume it has a somewhat similar setup as WdC regarding users. So it would be easy to see who uploaded the story and, in all likelyhood, was the author.
And even if some crazy legal dispute should arise and the beta reader stole the story for some unfathomable reason, the fact that you have an older version than the published one on your harddrive would be enough evidence to assert you as the legal author and owner of the story. (I'm not a lawyer, but plagiarism of this kind should be easy to counter)