There is the installation guide that came with OS X Public Beta hardly what your looking for. You can find good information by just surfing the forums and posting messages.
As for a manual I'm sure we won't be seeing any orgazined book of sort until the release of OS X and even then they will probably just package a simple get to know the interface guide and nothing that dives into using the Terminal and settings up a decent web server. We'll have to leave that up to a third-party to write a book. Which usually happens with new Operating System quite fast.
You can get a info about the GUI from the built in help utility, which downloads it's pages off the 'net as required. They dont give much detail though.
If you want to know about the CLI you can find lots of info on Linux/Unix sites. Most of the commands should be same or similar.
Linux sites will certainly begin to help you understand Unix.
Try http://www.linuxppc.com for starters.
Also goto http://www.apache.org for info about configuring the webserver.
The webserver in OSX is Apache!
But what are the real functionnalities of the 'Unix' interface (I mean the console)?
Can we build/compile some applications?
Are scripts possible?
What are the relations between this unix-based interface and the graphical interface of MacOS?
Can we take some linux sources and compile it under MacOS X?