Provide links to specific auto-generated API documentation within your package that is of particular interest to a reader. Doxygen will document pretty much every part of your code, so do your best here to point the reader to the actual API.
If your codebase is fairly large or has different sets of APIs, you should use the doxygen 'group' tag to keep these APIs together. For example, the roscpp documentation has 'libros' and 'botherder' groups so that those can be viewed separately. The rospy documentation similarly has a 'client-api' group that pulls together APIs for a Client API page.
Every ROS name in your code must be documented. Names are very important in ROS because they are the API to nodes and services. They are also capable of being remapped on the command-line, so it is VERY IMPORTANT THAT YOU LIST NAMES AS THEY APPEAR IN THE CODE. It is also important that you write your code so that the names can be easily remapped.