The downloaded metadata tags are usually not much of help (currently i've imported 100 books and have over 300 tags -- not the most useful tool to help browsing the library). Problem -- too detailed, too many of them. Although they are helpful then sorting the books manually.
But there's the "user categories" option available:
As i understand, the whole categorization mechanism is based on assigning authors\series\publishers\tags to a certain category.
So the only solution i see here is, then sorting books manually add some artificial tag, which should be clearly different from the downloaded ones, and used only for categorizing. Then, create the category and add that tag.
Ultimately the goal of this is to create a hierarchical library structure, where the structure is defined by me. I think this is what most people want -- the freedom to organize their library the way they want. I'm not talking about the actual file system structure.
Lets say i have a book "Microsoft Visual C# 2010 Step by Step".
So following my logic, i would place this book in "IT\Programming\Microsoft\". "IT" being the category, "Programming" it's subcategory, and "Microsoft" the latter's subcategory.
Or maybe there are easier ways to categorize books this way ? Drag and drop feature, or some kind of "add to category" option would be really helpful here.