To add such a note, you need to be signed in, and have editing rights for the paper. Look for the green Add editor's note button:
Resulting in something like this:
textile formatting is supported.
This is a very first step in providing more editorial control to paper editors - based on your feedback, we are looking into layout customization, branding, manual curation of individual content items and more generally being able to define precisely what should go into your paper and what not.