The Preferences Manager would be my recommendation. This allows you to save all your global JMP Preferences as a shareable .jsl file that can be distributed. Users can even toggle between "profiles" for their own personal preferences, and the managed org-wide preferences. If they accidentally change some preferences, they can use this to "reset" back to the managed preferences.
A more powerful approach would be to make and Share Platform Presets, which can also be mass-exported either as .jmppresets files, or as an addin. This allows you to customize more than just colors, and can be used for fully standardizing analysis and graphics.