(s)cgi-bin and all those other folders in file manager (Cpanel)

How on earth do you "link" whats in them to the main web pages?

At the moment every single file is in the "www" (Public_html) folder, but its so scatty and messy (a bit like this post, I'm sorry for that). I then wanted to install some scripts i.e "Users online" (http://www.lissaexplains.com/fun11.shtml), it told me I had to upload certain files to the (s)CGI-bin and create subdiretories etc, followed the instructions to the latter about changing the CHMOD but AHHH couldnt link to the contents of the folders.

I know this must be a nutty/easy question because I cant find the answer anywhere online! Please please just give me a link to a site which explains how to do it! Or even a guide, because AHHHHHHHH!