A family of Microsoft products that enable users to capture, organize, and reuse notes electronically.
Depends on where you save the notebooks.
If you save the notebooks in onedrive (Skydrive), its better to use multiple notebooks.
Each notebook is one file.
If the notebooks are saved locally in your PC, it does not matter.
Onenote will create a folder for each notebook and *.one file for each section in the notebook.
As long as the notebooks are in localy drive, you may organise them in any manner.