First, your files are stored in your mydocuments folder. I doubt they'll get wiped out when you install the full deal, but you can copy the whole folder elsewhere and then copy it back into place after the install and onenote will see those and import them.
Second, my instinct is that the commercial dvd will contain both the 64 and 32 bit installer. I'm doing some googling to confirm that, and I'll let you know if I do.
Okay this implies (at the very bottom) that the general office disc contains both installers on the same disk, and would make sense that the onenote disc would be the same. http://office.microsoft.com/en-us/wo...010369476.aspx
But my recommendation for full peace of mind is to query the Microsoft Answers forum: http://answers.microsoft.com/en-us/office/forum/onenote