How to set up COMPANY_DIRECTORY for multiple Business Units

We are currently on HCM Image 38/ PT8.59.04 and are experimenting with implementing Fluid Company Directory and Org chart functionality. We have approx 50 different agencies (Bus Units). When running the tree builder process for COMPANY_DIRECTORY, it requires an EMPLID to be specified. If the process is run for one agency (BU), it seems to work successfully using the top emplid for that BU. How do we add other BUs to the COMPANY_DIRECTORY tree? It doesn't appear we can have multiple COMPANY_DIRECTORY trees as the name must match the tree name in the Folder Administration. Thank you!