Right now the iPad/iPhone kind of treats Pages like a Flash drive with no folders.
You can look into 'Pages' using iTunes and it shows the projects you have. You can copy them to and from iOS devices and Macs but they're just copies. You have to keep up with which one is the newest version.
You can use their online iWork service, but it's pretty much the exact same thing...you just copy stuff and have to remember which one is newest.
The iCloud service will, I believe, do a better job at syncing things automatically and wirelessly and making sure you always have the newest version. I don't think (or don't know) anything about folders or directories with iCloud. It may still be a 'everything in one place' kind of thing, although I haven't used it so I can't say for sure.