I found you guys a partial answer.
If you go under ~/Library/Mobile Documents/ you will find the individual folders for Keynote, Pages, and Numbers (after you have opened them in your iOS device, of course). Within each is a folder named Documents. Save your files in there (I saved an alias on my Desktop for easy navigation to it). The apps will pick it up on the next sync. When it syncs, it converts the file to iWork online format. However...
You won't be able to open the file directly from the folder in your iWork desktop program. In other words, you can move the file from Mac to iOS, but not back without downloading it again and resaving in the Mobile Documents folder. Thus my saying it's a partial answer.
If someone comes up with a complete solution, let us know. We might just have to wait until an iWork update. Thanks.