The app designed to work with Onenote is called Mobilenoter. I tried it for several weeks and gave up on it. First it's a very limited program on the iPad, probably designed more for viewing but the main problem is the syncing. You have to manually sync and sometimes it just goes on and on with no indication whether anything is happening. I don't have a lot on notes to transfer so I can't explain the problem.
If you're stuck with Onenote because of work then you will probably have to wait for Mobilenoter to get better. I've found Evernote and converted over for every thing. The major plus on Evernote is the syncing. It's fast and pretty seamless. I have my iPhone, iPad, MAC and PC all synced and working. I really like Evernote, it's not a powerful as Onenote but it's not bad. You should take a look especially since it's free. I have to admit I tend to not pay attention to the free apps but it this case it would have saved me a lot. I pretty much bought all the note taking apps.
