Here are some sites with tips of how to organize your eBook collection:
- From PC Magazine: Get Organized: Tips for Managing Your Ebook Library
- From Adobe: Adobe Digital Editions App
- From Alfa eBooks: Alfa eBook Organizer Software
- From How-to Geek: How to use Calibre to organize eBooks
- From Macworld: How to use iTunes to organize eBooks
These are just several of the ideas out there for organizing your eBooks. Hope this helps.