Are you talking about the main nameserver settings for your server? Typically that is done during the initial server setup, but if you want to you can change that in WHM -> Server Configuration -> Basic cPanel/WHM Setup.
If you want a specific user/domain to have its own nameservers, you must ensure that the user for that domain is a reseller. Then as you are making them a reseller, you can specify what their nameservers are to be.
Your provider will need to add these for you so they will be used on every account you create automatically.
You will also need to create or register the name servers at your registrar if you haven't already and glue them to the IP's that your provider sets if anything other than the current addresses.
You will also need to create or register the name servers at your registrar if you haven't already and glue them to the IP's that your provider sets if anything other than the current addresses.