Wow! Things have really changed since I posted my comments 8 years ago. 
How do you annotate a game?
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If you're annotating within PGN files then you merely put your comments in brackets {Like this.}, between moves. If you're using HTML then you can separate comments from moves any way you like: different fonts, different effects, different colors, different boldness, whatever.
8 years later, you're a hero.