You aren't looking at anything magical, just a list of directories. This explains what some of the common directories are normally used for, but this can vary from system to system. Generally if you are doing web development you are only really interested in apache/php/mysql config files (normally located in /etc but sometimes in /usr) and the DocumentRoot directories of each virtualhost (usually specified in the main apache httpd.conf file though again it varies - debian in particular uses their own apache config system) - these are likely to be in www. The best thing you can do is track down the apache config and have a read to see how things are configured. You can find the fine by running the following if you don't know where it is (you probably need to be root un updatedb):
You may also find that as you're connecting via FTP what you're seeing is just a user's home directory in which case it is easier still, just browse through and see what's in each directory, there are no rules as to what is where.