There are two versions of OneNote that work with the Surface, and therefore one of the first things you have to decide is which version you want to associate to the top button of the Surface Pen. When you click the button, the version of OneNote that you associate to the button will launch.
The two versions are OneNote Touch and OneNote 2013, which may be best thought of as OneNote for Windows tablet (read Windows 8.1) and OneNote for Windows desktop. The desktop version has more features and is designed for use with a keyboard and mouse, while the tablet version has less features and is optimized for use with a pen.
For me the choice of which to use comes down to two relatively simple features. In OneNote 2013 you can set up each new note to have a default background (or paper), such as the lined paper that I use. Unfortunately, it doesn't appear to be possible to define a default paper for OneNote Touch.
OneNote Touch has a very handy menu for switching between ink colors and selecting features that displays by tapping and holding the pen, or your finger, on the screen.
I want both features in one version of OneNote, and I find it odd that Microsoft decided to not allow users to set a default paper in OneNote Touch, such a feature has obvious value in the tablet version.
While I really like the radial menu, I've decided that for quick note taking, which I think is the purpose for Pen top button button click, having lined paper is more important, and therefore I have associated OneNote 2013 with the Pen top button click.