Aperture is a database for managing a photographer's workflow. It is not a file manager (it does that as well) -- it is an image-manager. This is a rather high hurdle to set before beginners well-versed with file management.
Read the first seven chapters of the unusually well-done User Manual to get a sense of how the program works. Also take a look at my consise guide to the parts of Aperture and how they inter-relate (it is on the Aperture Discussions User Tips page).
Many of us went through similar frustrations when we started with Aperture. It _is_ different, and that difference requires adjustment on your part. Imho, it is vastly superior to using file managers to manage a photographer's workflow, but my telling you doesn't mean much. Try it, and try to work with it _the way it is designed to work_. I think you'll be glad, will use it with pleasure, and will never look back. But you are going to have to spend several hours learning how it works.
All that said, what you describe as how you want it to work, is, in fact, how it works. I can't tell what is not working for you, unless you are looking outside the database at files and not using the Aperture interface to look at Images.
HTH.
--Kirby.
(Sent from my magic glass.)