Configuring your own DNS Server with cPanel+WHM is really easy and recommended if you wish to host multiple domains in your cPanel server or you want to run a shared hosting environment. Having your own DNS server would give you flexibility of adding domains and then cPanel will automatically use your server to resolve domain names everytime you add a domain/website in your server.
(You can optionally use cPanel DNS cluster which is much better if you wish to have redundancy, load balancing  and failover DNS resolver, if you are only running 3 or less websites / domains consider using zoneedit.com's free DNS service to save on server resources or request our helpdesk for you to use our QuickWeb DNS Cluster)
Goal: Our goal is to setup something like ns1.yourdomain.com and ns2.yourdomain.com as your own name servers. Once your nameservers are setup clients can then use your own private nameservers for their domain resolution.
Requirements: cPanel+WHM root access, access to your domain registrar's panel, at least 1 IP address (2 recommended), bind DNS service must be running in WHM.
Note: yourdomain.com means the domain name you registered and must be substituted with your own domain name in real world eg. Â usa-hosting-stuff.com, this guide is not applicable if you are on shared hosting.
1. login to your domain registrar's management page for the domain, look for the function that enables you to create or register a subdomain or nameserver like ns1.yourdomain.com and ns2.yourdomain.com as nameservers. Make sure you point these to your cPanel+WHM server's IPs (point ns2.yourdomain.com if you have second IP address otherwise just point both to single IP of your VPS).  see this guide if you are with godaddy or http://www.youtube.com/watch?v=TbnEM2jdZjA
These registrations may take a few days to propagate (often as many as 3 days).
Once you can ping ns1.yourdomain.com and it is resolving back to your server's IP then we are now in business and can proceed to step no.2
2. Go to Basic cPanel & WHM Setup link menu link, skim to the bottom of the page to see the Nameservers which says "Here you can set the default nameservers used when creating an account."
Simpy put your own name servers in these boxes:
Nameserver 1 Box: Â ns1.yourdomain.com
Nameserver 2 Box: Â ns2.yourdomain.com
3. Save and you're done!
From now on everytime you will add a new client/domain these two name servers will be automatically configured, the domain will be automatically added to your DNS zone, your client or the owner of the domain should go to their domain registrar to change their name server and use your private name resolvers above... after propagation (about 6 -48 hours) the domain should automatically point to your server's assigned cPanel account.
