The annotations themselves are not stored within the web pages themselves, instead being hosted elsewhere, and inserted in to the page on load using JQuery. Annotations can be stored in your own storage system or using the free AnnotateIt service, also provided by the Open Knowledge Foundation.
The Annotator library is very extensible and includes default plugins for features such as user accounts, tags, filtering and formatting. An API is provided, allowing you to write your own plugins. Annotator is well documented and includes a plethora of help pages on the Annotator wiki.
To get started, you should read the Getting Started guide. To learn about setting Annotator up to use permissions with authentication, you should read the Authentication Guide, and the Auth Plugin page. If you want to store annotations on your own hardware, you should read the Storage Guide, and the Store Plugin page.
To see how our software is already being used in a system alongside Annotator.js, you can read about how the University of Mississippi’s School of Pharmacy use Annotator.js with our software here.