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One huge library is the way to go.
Use metadata, tags, saved searches, advanced searches to display the desired selection of books.
Maintain metadata. For e-books that do not have metadata, Calibre can automatically download covers, blurbs, series info and other data just by pressing Ctrl+D. You can even configure what resources should be used, and even install plugins for resources in other languages.
Please note that many people have much more than 1000 books and use one library.
Some of the few reasons for having multiple libraries are:
- One library for each language you collect books in (like English, German, Spanish)
- Fiction vs work documents (collection of manuals for example, or perhaps cookbooks)
- One library with proper e-books and the other with pdf files
- Separate library for books that are not processed yet into main library. You add metadata, check formatting, download cover, ... and then move the book into main library. Even that one I would implement by using a tag "___Not_yet_processed" (preceded by underscores, so the tag is always displayed at the beginning of the list of tags)
- Separate library for manga, comics, fanfiction
When I want to move a large number of books to the reader I use "save to disl" function of Calibre, so I can create elaborate folder structure by authors and/or tags and updates epubs and other format that uses metadata with the metadata from the Calibre database. Then I use function "create catalog" to make a nice internally hyperlinked document with books, authors, series, covers, blurbs that I can open with an e-reader and search / browse library on the reader.
Please note I use an e-book reader that supports hierarchical directories.
But ... it is your computer, use it any way you find convenient.
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