I'm not sure I have the full answer to your question. And I'm a bit unsure what you mean by "the org. workspace tiles". If that's the workspace as stored in desktop5.dsk, then I believe the answer is that it will be upgraded to desktop6.ndk if desktop5.dsk is present in the user's data folder at the point when they are setup up for Notes 6.
If it's Bookmarks that you're talking about then the file that needs to be 'seeded' is bookmark.nsf.
There's some discussion of something similar here:
If you are thinking of using roaming as well, then that adds another layer of complexity/possibility. It seems like by converting users to roaming at the right point you can have Notes handle all the user-specific stuff. The downside is that you'd probably have to run the install twice on each machine (first single-user, then multi-user). And that probably outweighs the benefit of not copying data to local profiles.
I've put up a draft procedure here for a roaming migration. It's probably unnecessarily complex, so I'm waiting for some guru to point out the flaws: