Change a sites docroot

Edit their file in /var/cpanel/userdata/.

vim /var/cpanel/userdata/proof/proof.shooltz.net

Change the docroot, and then run the following.

/scripts/updateuserdomains
/scripts/updateuserdatacache
cp /usr/local/apache/conf/httpd.conf /usr/local/apache/conf/httpd.conf.bak.before.duplicate.documentroot
/scripts/rebuildhttpdconf
/etc/init.d/httpd restart