Hey, you came back! Thanks!
To continue, what I have done to handle this issue is two part:
Family Files: I assign a unique naming convention to all custom or revisied family files. For my firm we choose a '#' prefix for all files we created or changed. If I am modeling away the time and see a family file in my model without a # sign prefix, then I know we didn't make it. If by chance I see the same family name with a # sign prefix, then I know I need to use that one instead. As an added benefit family files prefixed with a # sign will be listed at the top of their section in the Project Browser.
Directories: I also name all directories with a # sign prefix, telling the user that this directory is the company default structure. All families files/directories are stored on the server as well. On the server we also have all out-of-the-box content (under \Content of course) but in another main directory area. That content is not under the default directories users place in their Options File Search paths.
For example, you need to load a Detail Component. You fire up the Load dialog and you will be presented with all Firm family files. More than likely that is what you want, but on occasion we have not provided our own. In that directory will be a shortcut link to the same structure under \Content. The user can then click the link and will be in the out-of-the-box location.
I know this seems confusing so I will try to break it down again. There are 2 directory structures, A & B. A has the same organization but only contains Firm family files. B is out of the box. Within the A structure are shortcut links to the same structure location in B. The user's Options are all pointed to A directory structures.
That is the essence. If you don't understand it let me know and I'll post a pic of the layout.