If you use the same word twice, it counts as two words. Some people have shown me ideas where they have a separate map for the game; the rules mention something about different colours, and each colour is used multiple times on the map. (I approve of the coloured map idea.)
As explained in the rules & FAQ, 12 words are only for the core mechanics. You can have other sections, and it is fine to use as many words as you want in them.