WHM automatically generates your httpd.conf (usually at /usr/local/apache/conf/httpd.conf) and so any manual changes you make will be overwritten. To make changes open httpd.conf and under the correct VirtualHost check where the commented Include file path points, something like


Create a file and that directory tree and put your VirtualHost directives in there and save. Then rebuild httpd.conf by

/usr/local/cpanel/bin/build_apache_conf and then restart Apache 

/usr/sbin/httpd restart

and away you go. Note: This is for Apache 1.3. Apache 2 uses a different site-available/sites-enabled system