I stumbled across a handy feature in OneNote today. If you are reading a document and taking notes (I was studying for an exam) then switching between windows will soon become tedious. But - you don't need to switch back and forth between windows at all. In the Window menu there is an option to keep OneNote on top of other windows.
Doing this I found that I could work quite effectively with the X60 in slate mode on the train. I full screened the PDF I was reading and then put arranged OneNote over the top of the bottom third of the screen and configured the window to stay on top. I also found that using the panning hand in the PDF was the most effective way to re-position the content in the PDF - both pen flicks and the scroll bar had a tendency to scroll too far.