Have you created the nameserver entries with your registrar? Most of them have some sort of method for associating an IP with a nameserver.
Once that's done, you should just be able to type the nameservers in the WHM 'setup' screen.
You might also want to edit /etc/nameserverips to select the IP addresses you want your nameservers to have. There's also a method in WHM to do this: "Manage Nameserver IP's" There you just type the domain and it automatically selects an available IP address and gives it to the nameserver you specified.
Hope that helps.
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