In addition to Léonie's excellent advice I'd suggest one way of looking at what Aperture is and does is to focus on the idea of it as a Manager.
A comparison with the Contacts app is the best I've come up with.
The Contacts app is your Address Manager. This makes your addresses available to every single app on your machine. It's your point of contact with the addresses. Want to add one? Want to edit one? Delete one? Share one? All done via Contacts.
Now you can re-write that paragraph again. Aperture is your Photo Manager. This makes your photos available to every single app on your machine. It's your point of contact with the photos. Want to add one? Want to edit one? Delete one? Share one? All done via Aperture.
So, where the files are stored, while important of course, is a secondary issue because in the normal course of events you never access those files. You do it all via Aperture.
Similarly, with the Contacts app. Those addresses are all stored in a folder in Application Support, but that doesn't matter to you as you only access the data via the app or the various methods offered throughout the OS for integrating with it.
If the way in to Aperture is by importing, then the way out is by exporting. So, if you move a photo from project to project then when you export the project there's the photo - regardless of where it was stored on the HD originally.
So, decide on the file storage you want to use. Set up your back up system and forget about it. From there on you're working in the Aperture interface.
Hope that helps a little.