I must be missing something, right?
Right. 
If you really want to see the contents of the Aperture Library, right (control) click on it and select Show Package Contents from the contextual menu. You will then see your albums, projects, etc. The RAW files are stored within the projects (.approject) files. To view the contents of the .approject files, you will once again need to use Show Package Contents. Dig deeply, and you will find the RAW files, thumbnails and previews.
However, you should NEVER need to access your files this way. And you should NEVER mess with the file/folder structure within the Library, or Aperture will lose track of your photos.
Aperture is a powerful application. It is definitely one where you need to learn and understand it, either by reading the manual, or going through tutorials, or somehow. I strongly urge you to take the time to get educated on Aperture. It will save you time in the long run. Try the tutorials on Apple's website. There are a lot of them, and they will help your understanding immensely.
You can either allow Aperture to manage your RAW files by storing them within its own library, or you can store them wherever you want and tell Aperture to reference them in their original location. You don't need to store them in 2 locations, as you suggest.
If you want to Export files for use in other applications, them you can do that from within Aperture.
If you want to EDIT your files in another program (e.g. PhotoShop), you also do that from within Aperture. When you are done editing the photo in an external editor, Aperture keeps track of that edited version for you within its library. All automatically. All seamlessly (more or less).