The Planet have a little documentation about how to configure custom like ns1.mydomain.com DNS as primary DNS resolver in WHM.
Here detail explanation to do that :
1. Find your IP also secondary IP and setup your resolver Configuration / secondary resolver with your IP
So, let say your IP are 172.222.221 and 172.222.225. Also have yourdomain.com
At first WHM setup, you will read this :
Enter the ip address of at least two nameservers that you will use for dns resolution. Your datacenter should be able to provide you with at least one ip of a dns server you can access. If you do not know the ip address of your provider's local resolvers you should contact them. It is very important that these nameservers are correct, or you server will not function properly. If you do not know what to put in the boxes below and cannot contact your provider, please close this window and go though this setup at a later time; Your server should still function normally, however connections made to the server may be slower than normal.
Primary Resolver
Secondary Resolver
Fill your secondary resolver with your IP.
2. Set the server's current hostname under Networking Setup.
You have domain let say example.com and your main shared virtual host IP. Then we will make ns1.yourdomain.com and ns2.yourdomain.com (if you have secondary IP) as your primary DNS.
At Basic WHM setup, we see
This value should be a fully qualified domain name and will need to resolve properly.
Changing this value does not set the server's current hostname.
So,to change the server's current hostname, we go to Hostname function under Networking Setup.
Then under Networking Setup, change hostname for example stone.yourdomain.com rather than theplanet.host
3. Set the default nameservers as custom DNS on nameserver configuration under Basic / WHM setup
On Nameserver option , Here you can set the default nameservers used when creating an account. Change ns1.theplanet.host to ns1.yourdomain.com & ns2.theplanet.host to ns2.yourdomain.com.
Then save the option.
Remember, we will use yourdomain.com as primary DNS also custom DNS.