If the books have bad metadata, in the form of unusable tags, then that has to be fixed. Perhaps by copying them to an extra field "oldtags" and then deleting the tags, and add new.
Just add tags that are descriptive and that help you classify and find books. Calibre then let you set up searches for different combinations of tags. You can create a lot of virtual libraries for many different combinations. For instance fiction+crime+Rome but not juvenile. Or non-fiction+archeology+Greece. Or Reference+maps. And so on.
http://manual.calibre-ebook.com/virt...tual-libraries
But the hierarchy system may also be used. You should decide what type of tags to use at what level. For instance fiction/non-fiction/reference/periodical as the first level. Then followed by genre. After that location. Or perhaps location before genre? And so on. Maybe you could use some formal classification scheme, like one used in libraries?
Here is one example:
http://en.wikipedia.org/wiki/List_of...ecimal_classes
You can assign books to more than one position in a hierarchy. For instance a fictional book about an archeological expedition, with flashbacks to events at the time that left the traces that the archeological expedition is examining. It would be both contemporary and historical.
Read more about the hierarchy feature in the fine manual and experiment until you find some usable system.
http://manual.calibre-ebook.com/sub_groups.html
It is difficult to save books to a meaningful tree structure using tags or hierarchical classifications. It is best to keep the books in calibre and use that, or use a ebook reader that supports the tags calibre use. But it is not impossible to create a tree structure where the same book can be present at several places. One way is to allow duplicates, another to use different types of symbolic or hard links at the operating system level. But this is something that calibre doesn't support. You would have to fix that yourself.
Personally I mainly use loose genre classifications, and try to make them detailed enough so any classification is around 20-200 books. If there are too many books in one genre classification I divide it by making it more specific. A work in progress... Slow progress. :X
Fiction.Crime.Historical.Rome can be one such classification. I have a lot of historical crime novels...
Non-fiction.Archeology another. I don't have many books about archeology. If I obtain more I might have to be more specific.