The best way to use iTunes when you first start, is just set everything up in playlists. This will help keep duplicates out of the main library and probably help save your sanity.

Or, if you'd rather and all your music is in one main folder (with several subfolders?), just drag and drop the main folder into the main library window and let it load everything. Viola. You have a populated list without duplicates. Then you can create your playlists by selecting from th main library, and drag and dropping.