Site Name www.mysite.com
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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.