When I started using Calibre I went for tags in a big way, but as my collection expands I'm beginning to see the attraction of libraries - at the moment I've created libraries for Fiction, Non-Fiction & Mrs B's Books.
However, the classification system has yet to be invented that covers every case. For example, if you had a General/Literary library and Science Fiction library into which would you place A Clockwork Orange? I'd suggest that you need an entry in each. OK, you could place an entry in each library but you could save a little disc space if one of the entries could be a link to the other one. I strongly suspect that this isn't possible, and probably wouldn't be worth the effort of developing, but if you don't ask you won't get.