In this case you will have to do the entire stuffs manually…..
Consider your domain name as : x.com, user: xcom and NS you need to assign : ns1.x.com & ns2.x.com

1. Create DNS records for ns1.x.com as well as ns2.x.com
2. Now, open the file : /var/cpanel/resellers-nameservers from shell and manually enter the following :

    

   Code:

   xcom:ns1.x.com,ns2.x.com

3. Try creating an account from that resellers account and verify if the NameServers are the ones you wanted…