Sorry for the cross post (also posted this in another thread) but I think iCloud Drive is a Really Big Farking Deal. People have been crying about the lack of file system on iOS since, well, iOS 1. We finally seem to have one. I've been using iWork, Dropbox, and dropdav (to allow easy round tripping) and I am very excited to switch to iCloud Drive assuming it works well.
And if you look at the screen shots of it on Apple's site it looks like there are folders tied to specific apps, e.g. Numbers, as well as standard user created folders, like Household Finance. This bodes well, though I wonder if you could have a document mirrored in two places, like a spreadsheet from Numbers that also resides in the Household Finance folder. My guess is yes.
Also, I'd bet $ that iCloud Drive will be accessible from within Mail such that we will be able to attach files from Mail, and more than one at that.
Finally, my guess is that there will be a user configurable amount of storage to keep locally on iOS, like the last 1GB or 3GB or whatever worth of documents opened. And maybe you can flag specific folders or documents to always keep locally as well.
I think when all is said and done this will turn out to be one of the very biggest things announced at WWDC.