Hey Wyatt,
In AutoCAD (as you probably know) you must set support paths to your custom resources, menus, blocks etc.
Anyhow, in 2006 there are to new paths called Customization Files, Main + Enterprise. So, your cui files remain the same and are in the same location but the paths can change. For instance, if your Enterprise path is set to The cui file, then you will see that cui file as read-only and you will not be able to customize it. This is what you will want to do on user machines. You have a network shared cui file. All user computers pathed to that file as enterprise. They can use the company cui but they can not change it.
Now, if you path to that same cui file as Main, then you can customize it.
By default, acad.cui is the main customization file and there is no enterprise file pathed to.
My suggestion, if you are The Admin then keep your out of the box profile with acad as the main cui and set your enterprise path to your company cui file, rename the profile to whatever. That will be the user level profile.
Then make a new profile companymain, or whatever or your machine. In this profile, path to the company cui as main so that you (CAD Manager) can update it; also path to acad.cui as enterprise in this profile as well so that you will be able to use the acad menus also. Then you will switch between profiles depending on what you need to do.
Hope this helps?
Mark