The best way to learn is to use the system. For a good reference on the directory tree, i reccomend www.linuxcommand.org
. It's taught me everything i know about the command line and it has a good page on the directory structure as well. and its written in a way that everyone can understand it, no unexplained technical jibber-jabber.
Also, check out the Wiki that Snowpine posted a link to. it's a wealth of information