Aperture’s virtual filing/organisational structure can be quite intimidating when you first experience it, but as new as this seemed when Aperture first came out nearly two and a half years ago, it was firmly rooted in existing Apple software and concepts - iTunes (and to some extent, the Finder).

Aperture’s various ‘containers’ (Blue Folders, Projects, Brown Folders and Albums) fit quite closely to equivalent structures in iTunes.

Project = iTunes Library

It’s the main ‘home’ of images/songs (or videos, of course), it’s the place you go to to view all those images/songs. The basic building block, if you like. Obviously the analogy breaks down in places as you don’t have multiple iTunes Libraries open or searchable at once but it’s pretty close, and helps explain some of the constraints and limitations of images and Projects in Aperture.
For instance, importing images. Many people struggle with the ‘limitation’ that you always have to import into a Project (or an Album in a Project, more on that later). Think in terms of iTunes Libraries and it makes perfect sense - bring a song into iTunes, where is it going to live but in the main Library? You could put it in a Playlist as well but Playlists are pretty clearly just collections of things from the Library.

Albums = Playlists

While we’re talking about Playlists...
Albums make extremely closely to Playlists - they are both temporary collections drawn from the Project/iTunes Library and are not where things actually ‘live’. You can add the same item to as many Albums or Playlists as you want, and it doesn’t increase the number of items because Albums/Playlists only contain references back to the ‘home’ of the images.

‘I changed my image in an Album and it changed everywhere!’.
Yep. As we’ve seen above, there’s only the one Version, no matter how many places it appears - would you expect to change the name of a song in a Playlist and expect it to keep the old name in all the other Playlists it’s in?

In the same way, this explains the behaviour that confuses many people when trying to move images from one Project to another by dragging them into an Album in the new Project - as Albums only ever refer back to the originals, adding something to an Album will never move the original. To move the home of the image to the new Project you need to drag the images to the top level of that Project.

Tip - to copy the images instead of moving them you can use the same Option/Alt-drag as you can to copy items in the Finder and many other apps such as Keynote or Pages.

Smart Albums and Smart Playlists don’t really need any extra description, apart from the scope of Smart Albums being based on where they were created - if you want the Smart Album to search through the entire Aperture Library you need to create it at the top of the Library.

Folders = Folders

Unfortunately I can’t remember when Folders were added to iTunes, but the parallels are clearly there. Well, mostly.

Folders in both applications are there as ways of collecting together other containers - you can’t actually drag images or songs into them. Beyond that, they differ slightly in that Aperture has two distinct types of Folder while iTunes only has the one.

Blue Folders - these are mostly used for collection together multiple Projects, a function which has no equivalent in iTunes because you are only working with a single iTunes Library at once. Like iTunes Folders, selecting the Folder itself will show you the content of everything inside the Folder, making a convenient way to search through a set of projects at once.
Blue Folders can also contain Albums, and this is quite a useful way of making a Smart Album that looks through specific Projects - move a Project into the Blue Folder and the Smart Album will automatically add it to the search. Note that trying to import images into a Blue Folder-level Album won’t work - the Album isn’t in a Project, so there’s no logical way for Aperture to know which Project the images should be stored in.

Brown Folders - live inside Projects and therefore can’t contain Projects. The only thing they can contain is Albums. In Aperture 1.5.6 and older, selecting a Brown Folder didn’t show you the content of the Albums, this was only added in 2.0. Like Blue Folders you can’t add images to Brown Folders, they are just for collecting together Albums. In fact I wonder if Blue and Brown Folders should have been given some name other than ‘Folder’ as it makes everyone expect them to behave like a Finder folder.

That’s my take on it, anyway.

Ian

P.S. It's worth noting that the Finder (and indeed Windows Explorer, Linux equivalents etc.) is also a form of virtual organisation - when you move a file from one folder to another on the same partition nothing is physically moved - all that happens is that the files that keep track of which file is where are given the new 'folder path' of the file. So Aperture's internal organisation is a virtual structure on top of a virtual structure... ;-)