These things are all covered in the documentation. See Inspectors > Annotations & Reminders > Annotations in the built-in Help and manual.
and the type of document these are done within (markdown, formated note, HTML, pdf, text, rich note)
Annotation files can be used with any document in DEVONthink.
Also…
https://discourse.devontechnologies.com/search?q=annotation%20files
and …
https://discourse.devontechnologies.com/search?q=annotation%20files%20flyout