Change the Primary Document Root in cPanel/WHM

gistfile1.txt

For changing the main/primary domain, you will need to have root SSH access and be able to edit the following files (replacing your user & domain info):

/var/cpanel/userdata/USERNAME/DOMAIN.COM (replace USERNAME and DOMAIN.COM with actual info).

In that file, find these two lines:

documentroot: /home/USERNAME/public_html
path: /home/USERNAME/public_html/cgi-bin

And, edit them accordingly:

documentroot: /home/USERNAME/public_html/SUBDIR
path: /home/USERNAME/public_html/SUBDIR/cgi-bin

Save file, and then delete cache file for that domain:

rm -fv /var/cpanel/userdata/USERNAME/DOMAIN.COM.cache

If domain has SSL certificate installed, you would have to do the same for:

/var/cpanel/userdata/USERNAME/DOMAIN.COM_SSL

And, delete:

/var/cpanel/userdata/USERNAME/DOMAIN.COM_SSL.cache

Run these two scripts:

/scripts/updateuserdatacache
/scripts/rebuildhttpdconf

Restart Apache, and that should do it.

REF:
http://forums.asmallorange.com/topic/16797-best-method-of-changing-the-document-root-of-your-primary-domain/
http://blog.servint.net/2012/03/30/the-tech-bench-changing-a-document-root-in-cpanel/