If you are modifying an Apache configuration that is modified by CPanel, then you will need to use the CPanel interface to make changes.
Additionally, you will need to edit /usr/local/apache/conf/includes/post_virtualhost_global.conf to make any changes to the global configuration that fall outside of the scope of directives that CPanel can access.
Here are some sample configurations that you would want to add.
Alias /awstats "/var/www/html/awstats" <Directory "/var/www/html/awstats"> Order deny,allow Deny from all Allow from 1.2.3.4 Allow from 127.0.0.1 </Directory>
<Location /server-info>
SetHandler server-info
Order deny,allow
Deny from all
Allow from 1.2.3.4
</Location>
RequestHeader unset Range RequestHeader unset Request-Range ContentDigest On FileEtag None TraceEnable Off
HostnameLookups Off EnableMMAP On EnableSendfile On