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

/usr/local/apache/conf/userdata/std/1/USERNAME/DOMAIN/*.conf"

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