you should have let itunes add it to its directories straight from the drive. They're not appearing because itunes doesn't merely list the contents of its library folder, it creates a database so you can browse a lot faster. The database is non existent in your case because you just copied the files instead of "adding to your library" through the itunes menu.
My advice at this point would be to go into itunes preferences, uncheck the setting that says make itunes automatically copy the files into its own directories or whatever (to avoid a whole nother duplication of the files) and add the directory you put the files in to your itunes library through itunes' menu.