Decide how to organize your collection. Your ebook organization program will alphabetize your collection by title or author name, but there are other types of classifications you might want to mark: genre, year published, favorites, school or classics, for example. You'll be able to sort by any of these once you have finished organizing your collection.
Select a program to manage your ebooks. Calibre is free, can handle large numbers of ebooks, syncs easily with most ereaders and converts files to and from most ebook formats. The Alfa Ebook Manager is inexpensive and does everything Calibre does, but has a more attractive interface; it syncs with any ereader that uses SD/MMC chips for storage. Other ebook organizers include Brothersoft's Ebook Organizer and Adobe Digital Editions. Once you have your program selected, install it. If necessary, add your ebook collection to the program.
Download extended information on your ebooks by using ISBN numbers (the numbers below the printed bar code on most book covers). Each ebook management program includes a field in which you can input a book's ISBN, if it is not automatically imported by the program. Once the ISBN is assigned to an ebook, you can download the metadata automatically from dozens of online sources. Because the technique for adding this number is not identical for each program, consult the manual for an individual program's technique.
Metadata for each ebook includes items like the book cover, publication information and missing information of all sorts. While the metadata is not critical for organizing your ebook collection, it is useful for visual browsing and for capturing critical information you don't know like genre.
After your metadata has filled in what it can for your collection, go through your books and "tag" them with your special qualifiers. For instance, you can mark all the books from a specific series as belonging to that series or you can mark subgenres like high fantasy, comic fantasy and urban fantasy. Most programs use the "tags" field to do this through either a tag editor or by typing each tag into the tag field and separating them with commas (so you might mark "The Fellowship of the Ring" as "high fantasy, LotR, British"). Again, read the manual for directions for your specific program.
Prepare a collection for download to your ereader device. Type relevant terms into your search bar or use the search filter provided with your program; again, read the manual for the precise method for your ebook manager.
Download your collection to your ereader. Make certain all your ebooks are in a format compatible with your device. Use your ebook manager to convert any that are not compatible. Send books in compatible file formats to your ereader.