At this time you cannot organize templates directly inside the FCPX templates browser, but you can do this in the Finder.
Quit FCPX and go to your Motion Templates folder (user > Movies > Motion Templates). In the Motion Templates folder you will see different template type folders (Titles, Effects, Generators, Transitions). In these folders you will find your relevant custom templates.
When you delete a template folder here, next time you launch FCPX the template will not show anymore in your Effects, Titles, Generators or Transitions browser.
When you rename a template folder the new name will show in FCPX next time you launch it.
If you create a new group in one of the template type folders you can put any template that is relevant inside that group and when you launch FCPX the group name will show in the browser. When you select that group name all the templates inside the group will be revealed.
– Ronny