When it comes to organizing your notes, OneNote is all about freedom - you can put information wherever you want, move it around at will, and generally get totally lost. The search box is a lifesaver in this situation, but it's easiest not to get lost in the first place. Luckily, we've got four levels of hierarchy to play with in order to stay organized - what, you thought there were only three?
Folders - I use these at the top level, with separate folders for Work (everything I'm working on), Resources (useful information I might need someday), Secure (password-protected), and Blog (past posts and ideas for the future). Since the taskbar version of OneNote automatically saves everything into a top-level section called "SideNote", I've kept that section and use it as a short-term note-holder for random scribblings.
Sections - One level deeper. With default font sizes, you can fit about seven section tabs horizontally across a 1024-pixel screen, and that's also the useful maximum. Partly because you really don't want scrolling tabs - how will you ever remember what's there if you can't see it in the first place - but mostly because seven-plus-or-minus-two is the rule of thumb for "number of separate concepts you can keep in your head at the same time". So if you've got more than seven sections, start a new folder, and your memory will thank you for it!
Pages - Ok, I just counted, and you can fit 27 page tabs vertically down a 768-pixel screen. That's wayyyyy too many to easily grok at a single glance. Three ways to organize 'em:
You can find many more suggestions in Chris Pratley's excellent post, "How do you use OneNote?" Make sure you read all the ideas in the comments as well!
Part 1 of this series was about making your own toolbars.