You might like to take a look at this screenshot that I posted:
I discovered an interesting strategy for organising material over at the Tinderbox forums: the concept is “incremental formalisation” (Search results for 'incremental formalisation' - Tinderbox Forum). Stated rather crudely, the idea is that you don’t try to set out categories before you have done any work, but rather you begin working with the material and allow the organisation to emerge as you gain understanding of the material. This method perhaps works best with material that doesn’t obviously fit into rigid categories. But as you have discovered, it is not uncommon to find that material can belong in more than one place. One advantage of using tags, smart folders and the like, is that the work that one puts into organisation can be cumulative. Adding tags means that you preserve any work you have done before, whereas moving an item to another folder or group effectively “destroys” the previous work.