On a cPanel / WHM Server, you can add or change the private nameservers. However, when you setup an account through WHM, it does not show your private nameservers, instead it shows the default nameservers set by your hosting provider.
To correct this, you will need to modify the wwwacct.conf file.
ns = ns1.mydomain.com ns2 = ns2.mydomain.com
The new nameservers will now show upon new account creation with WHM using the administrator account.
But if you want to allow a reseller to use his own private nameservers too, go to WHM (usually located at http://www.yourserver.com:2086) and click on Reseller Center from the left column menu, under Resellers.
Under Reseller Modifications, select the reseller account from the drop down list and click on Edit Privileges / Nameservers. Scroll down the page and enter the private nameservers in the blank fields, next to Primary nameserver and Secondary nameserver.
Click on Save All Settings and you’re done!
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