If you'll only define an enterprise .cuix, you will not be able to save changes to your workspace. That includes which palettes are visible and where they are located on your screen. The enterprise cuix is always write protected, so users cannot modify it directly.
I'm managing a lot of client environment at our company and I'm using both the main and enterprise cuix. The enterprise cuix only contains the client specific customization, the main cuix is basically a copy of the standard ACAD.cuix but with a modified workspace to also contain the clients stuff.
Which cuix is loaded depends on how AutoCAd is started and with what profile. For each client I have a separate shortcut to launch AutoCAD with that specific client profile, which contains the support paths and cuix files for that client. But if you do not have different client environments but only a environment for your own company, you could do with just the standard acad.cuix and en specific company.cuix.
To setup just create a development AutoCAD profile, where the main cuix is your company.cuix and the enterprise is the standard acad.cuix. Next step is to fill your company.cuix with the customization that you want to have.
After you've added all the things you want to have in your company.cuix, now setup your working environment. So turn on/off the toolbars (if you have/want any) that you want to have and position them at the right spot, rearrange the ribbon to show the tabs and panels that you want to have, turn on/off and position the palettes that you want to have by default, etc.. If you are finished with that, save the workspace to a new name i.e. your company name. The workspace will always be saved to the main.cuix in which in this case is your company.cuix in your development profile.
After this is done create a new production profile where the main cuix is the acad.cuix located in your current Windows profile and the enterprise is your new company.cuix (make sure this one is located on a shared network location) and make all the necessary changes to the settings in the profile.
Now export your profile and store at i.e. at the same shared network location as your company.cuix.
The other users now only need to import the saved profile and make it current to get the customization and company workspace. Any changes the user makes to toolbars, ribbon, palettes, etc. will be saved in the main cuix which is their own acad.cuix and they can create their own workspaces with the customization from the enterprise menu.
If you want to make any changes to the company enterpise cuix, just use your development profile (with if correct your local mastercopy of the company.cuix) and test it. If everything is ok, just copy the modified company.cuix to the shared network location and all other users will have the new .cuix when restarting AutoCAD. Beware that if you make modifications to the workspace, the users will need to re-select the workspace to get the changes and this will discard any changes they mde themselves and did not save into a new separate workspace.
Important: make sure only you have write access to the shared network location and all others have read-only access, as this will protect your customization from changes by other users if they try to tinker with it.
Hope this long story makes sense to you.