My solution is this, in Microsoft Word, I've created a style called "Clues". The format of the style is exactly the same as the "regular text" (Normal). Hence my naming this an "invisible style" as to the naked eye, it would be impossible to distinguish between these two styles.
You may ask, so what is the whole purpose of this? Well, one of the things that people don't realize is that with Microsoft Word, you can actually search for special characters, characters that are not view-able - not regular characters. Using this advanced "find" ability with Word, I can also have Word temporarily highlight the text that it finds, so if I search for the "Clue" style, there we go, all of the sections that contain clues are highlighted. In this link, you can read one of my previous blog entries that also relates to this tip on searching by special characters for more details on how to use it.