I’m a huge OneNote user at the office. I use it to keep track of all client information, including correspondence, research, emails, documents, and notes. I specifically purchased the HTC Flyer and Magic Pen to take notes during client interviews, at meetings, and at other times during the day when I am away from my desk. I wasn’t sure at the time, however, how I was going to get those notes into OneNote.
The Flyer has nice EverNote integration, but it doesn't support OneNote. But after a bit of searching I found Ever2One Converter, a little desktop program from MobileNoter that simply exports EverNote files to OneNote. An article from How-To-Geek explains the process. If you’re a OneNote user like me it's certainly worth checking out.
You can also import notes from EverNote via Outlook (send the notes via email and import them in Outlook using the send to OneNote button), export notes from EverNote as HTML and import them into OneNote, and import notes from EverNote using the OneNote Printer. While all of these options will do the trick, I found the Ever2One Converter method the easiest to use.