You have something very similar to what we are using, so I'll outline that:
Enterprise (in read-only network folder): custom file with commands for our common in-house functions
Partials, under Enterprise (in read-only network folder): acad, raster design, express, Cloudworx, and some other third-party stuff
Workspaces defined in Enterprise: a few basic starter workspaces the users can begin with
Main (in per-user read/write network folder): custom file, completely empty
User created workspaces will be saved under the Main
The Main CUIx could easily be on the hard drive, but their personal network drive is backed up nightly and the hardware can be reformatted or even replaced and they still have their personalized workspaces. The development process:
- start wtih a blank CUIx for the Enterprise and set it in the "Main" slot so you can modify it
- fill the Enterprise with custom commands
- add ACAD, Express, RD, etc. as partial to the Main
- verify everything is available, build starter workspaces (toolbars on/off, Ribbon tabs and panels, etc.)
- create a new, blank CUIx for the Main
- change the Enterprise from the Main "slot" to the "Enterprise" slot, and put the new (blank) Main in the "Main" slot
- do any customizations you want to the Main (this will be copied to each user)