1. Select the location of the XDoclet files other than root of the project. Sorry, this might be a case of RTFM, but I have fonud nothing obvious
A MyEclipse project can only support at most a single xdoclet build file, i.e., xdoclet-build.xml. To do more than this you must set up and maintain addition custom build files.
2. [Potentially] run multiple XDoclet configurations in the same Eclipse project. I am assumming this is not possible at the moment. Is there a plan to extend support in that area?
Your assumption is correct. This is the first request for support for multiple XDoclet configurations per project. Our assumption is that a project would typically contain a unit of code for which a single configuration would apply. Beyond this scope the operation and development complexity begin to grow significantly.
Michael
MyEclipse Support