For the main domain, the only way to change the path would be in /var/cpanel/userdata/username/domain.com file where domain.com is the main domain name. You'll documentroot and homedir paths there for the location where the main domain is served.
If you edit that file, you will need to run the following commands to update the paths:
I highly suggest making a backup of that file before you edit it:
cp /usr/local/apache/conf/httpd.conf /usr/local/apache/conf/httpd.conf.bak111114
Above wherever username is mentioned, this stands for the cPanel account username. Wherever domain.com is mentioned, this represents the main domain on that account.
cp domain.com domain.com.bak111114