Thanks to the help from our friends at beetlewebs.com we've managed to do this lovely little tutorial for you to help you get your domain added to your cPanel account.

Errors:
(XID 3cjrqh) The domain “sub.domain.com” already exists in the userdata.

(XID n572vd) The domain “sub.domain.com” already exists in the Apache configuration.

(XID kejmhu) A DNS entry for the domain “sub.domain.com” already exists.

How to fix it:

Go to: nano /var/cpanel/users/**Username**

Remove the subdomain from the DNS list and re-number the others like so:

DNS=domain.com
DNS1=domain2.com
DNS2=sub.domain.com

Then go to: cd /var/cpanel/userdata/**username**/

and remove the domain files like:

rm -rf ./sub.domain.com
rm -rf ./sub.domain.com.cache

Next we need to remove the domain from the main files. Go to: nano ./main

and remove the domain from the sub_domains:: section.

Then on the ./cache and remove the line for the domain like: sub.domain.com: username==root==sub==domain.com==/home/username/public_html/domain.com==***.***.***.*:80======0==

And then restart the services:

/usr/local/cpanel/scripts/updateuserdomains
/scripts/rebuildhttpdconf
service httpd restart