By default a cpanel account will have it’s domain point to /home/username/public_html but if you want to change it to point to a separate folder, you would just need to ssh in to the server and edit these files:
vim /var/cpanel/userdata/USERNAME/domain.com
vim /var/cpanel/userdata/USERNAME/domain.com_SSL
So just replace USERNAME with the cpanel username and domain.com with the actual domain. But in those files you would change:
documentroot: /home/username/public_html
to:
documentroot: /home/username/public_html/some/other/folder
Save that, then first make a backup of the main apache configuration file:
cp -rp /usr/local/apache/conf/httpd.conf /usr/local/apache/conf/httpd.conf.bak
Then have the system rebuild apache’s configuration:
/scripts/rebuildhttpdconf
Then finally restart apache:
service httpd restart
Then the domain should start resolving to the new documentroot path after that.