Many people have wondered how OneNote 2007 and Groove work together (or not). Your experience will depend on whether you're using a Groove Workspace or a Groove Folder Share. Here's a brief summary. I'll write more later, but suffice it to say we're aware of the limitations and have grand plans for dramatic improvements in the future...
OneNote experience with Groove Workspaces will be limited / problematic
OneNote experience with Groove Shared Folders will be much better but still have conflict issues
Basically Groove works okay for single file document model (but still has conflicts) but it can be quite problematic for data that is represented by sets of files. OneNote Notebooks are an example, Front Page webs would be another example (although obviously less frequent).
Given the time remaining from the point at which Microsoft acquired Groove until the release of OneNote 2007 and Groove 2007 we were unable to do more to make this better in this release because it requires some architecture changes. But it's high on our list to make much better in the next release.