I'd like to get an idea of how others may have implemented Zendesk amongst their departments/areas. Was a user field, type dropdown list, called department with a list of departments/areas? Or was an organization created for each department and a user field created (Type: Lookup Relationship - Organization) called Department/Areas?
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It seems your use case with developing departments using custom objects or organizations can be related to New Custom Objects EAP. Please follow this link.
Hope it helps