Use a real version control system for version control -- I'd suggest mercurial or git. Pretty necessary if you are going to take advantage of continuous integration anyhow.
What we use is really about 3 instances per site, servers aren't quite a 1 to 1 map. We keep:
a) ci.whatever.com -- the continuiously integrated version of the site. Really for developers to make sure their changes didn't break anything someone else did, also handy for quick feature feedback from end users or stakeholders.
b) qa.whatever.com -- much more checkpointed version of the site. For final QA / approvals.
c) www.whatever.com -- the real deal site.
We typically don't bother with a popup like facebook because we can usually accomplish the update in a matter of seconds -- we just update the codebase in production from the appropriate source repository and run the database scripts. Facebook's build and deploy process is a bit more involved, but I saw an article recently on it. You might want to google around a bit, I can't recall where I saw it though.