Based on the tone of the question, I'm assuming you are a Cloud customer? I *think* the answer with Cloud is that it is not very easy to do. I think you'd need to plan it for over a weekend, and people would see you working on it unless support could help you put it in maintenance mode with a back-door URL for the design team to use for set-up.
Thanks for your reply Tracy! I've made quite a bit of progress on this today. I have found the theme engine and I believe I've found what I need.
For anyone's future reference:
Admin>Themes - There you can create themes and only publish when you are ready.
This doesn't solve for the Jabber/Webex integration, but is a big win for the interface side.