Relationships - how to automatically link departments

Hi, We import users and departments from AD. My questions is how to programmatically create relationships so the departments link together right up to the Department Head (in this case Jon). In the attached image, Users in the red department (under Rod) appear in the relationship diagram, while users in the blue department (under Grant) appear in their own relationship diagram but while the 2 are part of the same group, I can find no way to link them together apart from manually creating a relationship. Additionally, the Department Group manager (Jon) is not linked to anyone as his department name is different to the red and blue departments. Ultimately, I want to set the highlighted Group Manager (Jon) as a Department Head so we can use more of the automated tools. Apologies if the attachment doesn't come through or appears 3x - I have had issues trying to upload it
Chris White