Your question is too thin on details to be able to answer directly.
What is it you're trying to do?
If you're using Mac OS X Server and Apple's Server Admin application then, for the most part, you can ignore Apache's web site and use Apple's documentation itself - Server Admin provides a GUI front-end to configuring most of the common features in Apache, so you can create any number of sites with just a few clicks.
As for the file structure - web content can be stored any directory you like. Sure, Apple's default is /Library/WebServer/Documents but you could put content anywhere. Some people create additional directories at /Library/WebServer (e.g. /Library/WebServer/Site2, /Library/WebServer/otherdomain, etc.), while others might put it somewhere completely different (with /var/web being another common choice). At the end of the day, it's up to you.