By default, iPhoto stores photographs in folders according to their dates as recorded by your camera. If you are one of those nitwits who never set the date and time in your camera, then iPhoto's folders may not make a lot of sense. You are, however, free to establish albums and to place each photo into whichever album you like.
I see what you're saying, that never affected me because I always kept the original and saved the edited ones elsewhere. Photoshop CS has a much better file browser but you still need to navigate through iPhoto's directories.