I always thought of manuals as an afterthought both in developing a game and actually playing a game. While a back-story would be nice, it should also to be possible to play a game without having to touch the manual.
Saying that, I think you should write your game before writing an actual manual. Your interface may change, your story might change, or you might decide that you want to make it a shooter instead.

By all means write notes so your story is consistant throughout the game.
One time, when I was a kid, I used to write the description of a story that appeared on the back of a book, before actually writing the story.. it's the wrong way of doing things.

- Nick