Issue :

The main domain and the add-on domains need to be on different dedicated IPs.

Fix :

This cannot be done directly through cPanel/WHM .
If suppose your cPanel account username is “USER” and domains are:

maindomain.tld
addondomain1.tld
addondomain2.tld

Then you have to edit the following files using vim or pico editor :

/var/cpanel/userdata/USER/maindomain.tld
/var/cpanel/userdata/USER/subdomain1.maindomain.tld
/var/cpanel/userdata/USER/subdomain2.maindomain.tld

And change the IP field to in each to your desired one.
Then you have to rebuild apache using /scripts/rebuildhttpdconf
Restart apache service.
Edit DNS zone file of each domain and point A record to the new IP.

That should be it! All your domains should work flawlessly and you should also be able to install SSL , if required.

Issue :

webmail.domain.tld does not work.

Fix :

1. Create an ‘A’ record for the sub-domain ‘webmail’ in the DNS zone file. It should look like :

domain.com. IN A XX.XX.XXX.XXX
localhost.domain.com. IN A 127.0.0.1
domain.com. IN MX 0 domain.com.
mail IN CNAME domain.com.
www IN CNAME domain.com.
ftp IN A XX.XX.XXX.XXX
cpanel IN XX.XX.XXX.XXX
whm IN A XX.XX.XXX.XXX
webmail IN A XX.XX.XXX.XXX
webdisk IN A XX.XX.XXX.XXX

2. Put the following code inside .htaccess in the sub-domain folder ( virtual sub-domain which doesn’t have an entry in httpd.conf

RewriteEngine on
RewriteCond %{HTTP_HOST} ^webmail.domain.com$ [OR]
RewriteCond %{HTTP_HOST} ^www.webmail.domain.com$
RewriteRule ^.*$ “http\:\/\/domain\.com\/webmail” [R=301,L]