Although it is a slightly different implementation, what you are looking at on NarutoWiki is more comparable to the age-old Category feature. This requires that you add tags to each article that can be filtered by. E.g. Crystal Armor would have at least:
If you nest your Category pages in the same way, and link your main categories from a front page, you can set up a nice filter system this way.
Books are more for content where the order the user reads the pages generally matters. A Book will have an ordered table of contents of everything inside it. You can only have 1 Books forum (with many books), but the pages in each book can be saved in any forum.
Either way, you don't have to start your wiki completely over, but you'll have to go back and update the pages you already made.