As far as I know, ProjectBuilder or Xcode can only create bundled
applications that get rid of the need of resource fork. rsrc files have
their data in the data fork (however, the resource manager can manage
the two types of resource files, old version with data in resource fork
and the new one with data in data fork).
If I quite understand you, you want to add a resource fork to the
executable (hence the file in the MacOS folder of the application
bundle) but what's your goal ?