Hello Graham,
For two CODM organs to be considered distinct by Hauptwerk you should just need to make sure that the following settings in your CODM ODFs are different for each of the two files:
_General.UniqueOrganID
_General.Name
_General.OrganDefinitionFilenameExcludingExtension
Hauptwerk saves its organ-specific user settings relative to the unique organ ID, so if you make two organs with the same ID then the settings from one will overwrite the other. Also if you make two CODM organs with the same OrganDefinitionFilenameExcludingExtension then the compiled ODF from one would overwrite the other.