Forget the library in finder exists. Do not "clean it up" -- you WILL corrupt and/or lose photos. Do anything and everything to/with your photos from within the iPhoto app. Or, do NOTHING within the app and do everything in the library (and use some other viewing, organizing, editing software -- just not iPhoto if you mess with the library in finder). The app and the finder do their things on their own, and do not like to be messed with.