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I think that the OP was asking about organizing books within a calibre library.
Calibre organization is based on book metadata (that's the information given in the columns for each book). You can add or edit the metadata by clicking on the field you want to edit or by selecting the book and choosing Edit Metadata. To edit the metadata for multiple books at once you select them and click on edit metadata Once the books are properly tagged you can then search for what you want by using the tag browser or search bar.
A simple way to organize your books would be to tag them as category.subcategory since the tags column allows for subsets or hierarchies by using a period (for example I tag a book as 'history.modern.19th century' and when I click on tags I can choose to see all my history books or just the modern history books or just the 19th century ones). You can also allow for multiple tags by separating them by a comma (so my 19 century history book may also be tagged as art or cooking and yes I do have a 19th century history book with recipes as well as a rather academic art-book on Impressionism in its historical setting) which is the main advantage of tags over folders.
Virtual libraries are a bit more involved but they also depend on metadata. Their main benefit IMO is that you can set up virtual library tabs and searches within a virtual library will only include books from that virtual library (so if I have a virtual library set up for my history books a search in that library for science books will only yield old classic science books and history of science books not current science books).
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