/etc/apache2/sites-available/ hold all available sites with 1 file per site. The domains are inside the files.
/etc/apache2/sites-enabled holds the sites that are active. Again: the domains are inside the files. These files can be symlinks to
AddHandler cgi-script .cgi
CustomLog /var/log/apache2/access.log combined
Try to keep files outside of
/var is often not a separate partition and is also used for storing printer files and mysql files so if any of these 3 make it fill up your system using the machine to fix this problem might be more difficult than needed.
It also makes it easier when you need upgrade or re-install your system, add more space to your system or need to use several different operating systems.