Still experimenting myself on a good setup, but I did have a thought to the structure:
Organisation level = All DGNLIB, SEED, settings, etc relevant to a client (for me that is IL Tollway)
Workspace = Project level (old PCF area)
Workset = Groups of similar DGNs within the same project. Example, Workset for SUDA drainage, Workset for Modeling of Zone 1, etc.
Thoughts or opinions on this? The natural fall of the program seems to want to do this.