After you have imported alot of stencils, your STENCIL LIBRARY will become a mess.
For illustrative purposes, we have put a screen capture sideways, showing a third of the STENCIL LIBRARY after approximately six months of using OmniGraffle for an ordinary user.
This is quite messy but very easy to fix.
Right-click on any of the stencils and select the Show In Finder menu command:
All you have to do now is create appropriate folders and move corresponding stencils into those folders.
If you create folders with the same name as the built-in folders in OmniGraffle both your imported or created stencils and the built-in stencils will be available in those folders.
In the screenshot shown next you see the Stencils folder after the re-organization and on the right the STENCILS FOLDER in OmniGraffle.