If you missed the basics of my library organization, you can find it HERE.
The second part of an organized library is MAINTAINING the organization. I can honestly say that I spend no time maintaining my library. I take time training my students on proper use, and I have a librarian as one of our class jobs. Other than that, the library is completely self-running.
Each of my books is stamped with my name (I got this one on Amazon: One Line Custom Rubber Stamp (Black) ) I used my Excel spreadsheet to do a mail merge in Word and create labels for each book. That way, every book has a labeled card.
To create a system for students to check out books, I glued some decorative library pockets to a large piece of poster board. I laminated the whole thing, and then used an exacto knife to cut slits in the pockets. It takes a beating, but it can last for a couple of years this way. When students want to check out a book, they simply put the card from the book in their pocket (my students each have numbers). When they check the book back in, they put it back in the pocket, and get it back to the right bin by using the sticker on the back of the book (see previous post).