Start a fresh copy of Geneious Prime, set it up the way you want. Shut down and then copy Geneious 2019.0 Data/user_preferences.xml to the Geneious install directory (e.g. C:\Program Files\Geneious Prime on Windows) and rename it to default_user_preferences.xml. On MacOS the ﬁle needs to be in Geneious.app/Contents/Java (R9 and above), or Geneious.app/Contents/Resources/app (R8 and earlier).
Now, when users start Geneious Prime for the ﬁrst time, they will get the conﬁguration you set rather than the normal default.
Examples of features you can change:
Any users who have already run Geneious should click the “Reset All Preferences” button in the Geneious Preferences to load these defaults.