Hibernate support in MyEclipse has not been fully developed yet. It only supports creation of hibernate configuration, setting up libs, and reverse-engineering from database tables at this time. The more advanced features you are looking for will come in a future release.
For now, you are expected to keep the POJO and mapping files in sync once generated. If you regenerate the mapping file, your changes will be overwritten, so be warned (as it notes in the file itself). The POJOs come as an abstract base class and concrete subclass – you can do what ever you want with the subclass as it is only ever generated once. The base class is regenerated if you regen the mapping.
Currently, there is no direct support for xdoclet hibernate tags for the Hibernate tools, nor is there a plan to support same.
jeff