Site Name    www.mysite.com
==============================

DocumentRoot /var/www/www.mysite.com/content
ScriptAlias /var/www/www.mysite.com/cgi-bin


Ok, if you use the layout as above you would normally put your index.html in /var/www/www.mysite.com/content 
and your scripts in /var/www/www.mysite.com/cgi-bin

When you goto www.mysite.com you load the index.html from this folder.

If you have images in your pages, and the link is for example    /img/logo.gif  then the files should be in /var/www/www.mysite.com/content/img

You do **NOT** put the full path to the file as /var/www/www.mysite.com/content/img/logo.gif
You only start within the documentroot, as only your server knows that the site is stored here.