"Read the design guides" - heh... that's a good one Simon! Unless you work for Cisco of course...
I spent way too long looking for informative documents on this issue on the Cisco website, and that was with PICA access to the TAC knowledge base. D, if you need help designing a Call Manager cluster integrated with AD, then make sure you go straight to Cisco for advice - and I mean in person. Don't trust the (often out of date or simply misleading) documents you'll find on the CCO

CCO is good for an overview and for reference, but once you know what you want, get a Cisco representative to sanity check your ideas and add detail to the final solution.
To answer your question more directly, CM doesn't integrate with AD at all, unless you install the plug-in Simon talks about.
Apparently this plug-in which allows integration with AD is a bit problematic on anything other than CM3.3 and that's coming from our Cisco representative. Our Gold partner doesn't even want to touch our install in case the integration breaks basic functionality (we're currently only on 3.1 - not a recommended platform for AD integration)
Other aspects can also be problematic. Our split domain
is supported by Unity, for example, but only if you follow strict guidelines about where the server is located, where your Exchange server is located, what usernames are used for services (and their rights to the domain) and what usernames are used to login.
As for where the server sits on the domain, it's usually as a stand-alone server, but we later added into the domain without too much difficulty. The biggest "gotcha" was that once we'd added it the DHCP stopped working - it wasn't an authorised server! Once that was sorted, things went fairly smoothly. This integration into the domain allowed us to run IP Operator Console and read in the names of our Global Directory from a share on the CM without having to recreate our AD users on that box.
Hope this helps.
Good luck!
Neil.