Where and how Aperture keeps original image files, referred to as masters, is a topic of constant discussion and for some - constant confusion. I hope to shed some light on the topic for new users and maybe show some old dogs a couple of new tricks in the file management department. Starting at the beginning Aperture allows you to choose two different approaches to managing your original image files. The first way is called "managed" masters. If you choose to use "managed" masters Aperture will automatically copy all of your original images from their import location into it's own library, you don't have to worry about a thing. For some reason this scares people and makes them very uncomfortable. I have no idea why. The Aperture library is just a folder with an attribute that tells the finder not to let you see inside and accidentally screw it up with out doing something really special and complicated (right clicking). If you do not need multiple hard drives to store all of your images this may be the best way to get started. I promise you can get your images out no matter what. Don't worry. I use managed masters on my laptop all the time. It's convenient, cleanly, and fun, but more importantly it is really easy to back up to a vault while you are traveling.
The second method that Aperture provides for storing your original images is called "referenced" masters. Using referenced masters means that you are responsible for choosing the location that your original images are stored. You are also responsible for backing them up, they will not be stored inside an Aperture vault. From my perspective the only reason to use referenced masters is if you have a really good reason to. One good reason is that all of your masters will not fit on one drive. Or at least they won't fit on your laptop drive and you would like to take your whole library with you sans masters - more about this in a bit. Reasons other than this are shaky at best. Reasons like "I like to get at my originals" - My question is to do what?
Moving along, there are a couple of basic functions that you need to know about in order to "get it" when it comes to dealing with where your image files live at the moment. I say "at the moment" because this is not at all a thing that you pick once and it is written in stone. You can move your files around any time you like, you just have to know how. Having said that, the first place that you can choose where to store your images is in the import window. You have three basic choices. One - put them in the Aperture library. Two - leave them where they are right now. Three - copy them to a location that you specify. The first one is managed masters, the other two are referenced masters. That's it if you never ever want to change anything down the road, and your system never changes, and you like things to stay exactly the same. The real fun begins when you realize that where images are stored is not a one time choice at import time. This leads us to the other couple of tools that Aperture provides for managing image storage location. There are only three. Consolidate masters, relocate masters, and manage referenced files. All of these are in the File menu.
Starting with the first one in the list, Consolidate masters, simply tells Aperture to bring all of the files no matter where they are into the Aperture library. This is more useful than it appears at first glance. For one thing if you like to take your entire library on the road but cannot fit all of your masters onto one laptop sized drive you can selectively consolidate masters only for projects that are "active" in some way and have previews for the rest (or not). The next on the list is relocate masters, this works on any images, referenced or managed, or a combination of both at the same time. Using relocate masters you can tell aperture where to move masters in your storage scheme. If the images are managed masters it will relocate them from inside the Aperture library to the location that you specify. If they happen to be referenced masters the will be moved to the new location specified. But wait there's more… In the process of moving the masters you can have Aperture automatically put them in folders based on the project name that they are in, a couple of different date formatted folders, and a bunch of other options. It will also rename the masters to your unique needs. The thing that is really funny is that I run across people all the time that are trying to fight Aperture by doing these things manually instead of just letting Aperture do it for them. Why oh why? They get nervous that they the logical organization structure within Aperture does not HAVE to match the folder structure where the master images are stored. It can, it just does not have to. Most people run into problems when they try to force Aperture's logical organization structure to match the folder structure of referenced images. They do this by trying to arrange Aperture's internal organizational structure and then manually maintaining the folder structure where they keep their masters and trying to keep the two hooked up with the third function "manage referenced files" that we haven't discussed yet. If you want the folder structure where your masters are stored to be meticulously organized and match your logical organization within Aperture use relocate masters to do it or if it is so sacrosanct (it's not) make sure that it is good to begin with.
Now for the last function, manage referenced files. You will be better off thinking of this function as a disaster recovery function. The less you need to use this the better. To be very critical of Apple, the user interface for manage referenced files is a disaster in terms of clarity. Once you know exactly how it works via the school of hard knocks and bloody noses it's actually pretty smart in the way it goes about doing things but… it is not a function that you want to be using in your daily work-flow. The bottom line is that this function is for occasional use only. If for some reason your referenced masters get unhooked from Aperture this is the function that you use to hook them back up. In most cases this will be a horrific accident caused by you. On occasion you may want to do this on purpose, mostly for reasons of efficiency like moving a bunch of your masters from six 250 Gigabyte drives to one 2 Terabyte drive. Do yourself a favor and backup your library before doing this in case you get it wrong so you can get back to where you started. The one secret to making manage referenced files work is that you need to select all of the files in the upper pane that are disconnected and then navigate to the correct/new location in the bottom pane. Doing this will activate the "reconnect all" button that will do all of the heavy lifting for you.
That's a lot of information in what is hopefully the shortest amount of space possible. The real power of these three simple functions is when you realize two things. The first being that managed or referenced is not an all or nothing proposition. The second is that the images that you apply these things to do not have to be project by project, they can be any selection using any criteria that you wish. An example of the first idea I have already mentioned, if you would like to take your entire library with you but cannot fit all of the masters onto a laptop sized drive then you can have a mainly referenced library and use the consolidate masters function for only the projects that you would like to work on while you are away. While traveling you can import using managed masters for simplicity. When you return to home base just copy your library back to your main machine and use relocate masters to put the masters in their final resting place (or until you want to bring with again). The second idea is just as useful going the other way if you have mainly a managed master library but want to trim down it's size use whatever criteria you would like to make a selection in the all photos view. Let's say anything older than a year and less than three stars. Select all of the images and use relocate images to put them nice and neatly on an external drive with whatever anal-retentive folder structure you would like. Using this and the ability to manage the crap out of previews can give you a ton of flexibility in trading off library size vs. utility.
I hope that this clears up some confusion for people not accustomed to Aperture's storage abstraction and gives a couple of idea for those of you that are. If there are some specifics on any of these functions that you need some clarification on just drop a comment or an email and I will do my best to make it as clear as I can.