What you're doing is right in line for what many people do. The downfall being that if one of your nameservers stop working for whatever reason, if they're on the same machine BOTH stop working which means that your sites won't display. Nameservers stopping in cPanel is actually a fairly common event minimum of once per month sometimes more frequently depending on what is being done on the nameserver side of things.

So you'll setup the information in your WHM and assign the IP number (under the section for Setup Nameservers). With the IP numbers that it provides you then go to your registrar and tell it that ns1.mydomain.com points to whatever IP number.

Getting the domain name to use the nameservers on the server will basically mean you just change the nameserver information on the domain name itself to no longer use your hosts nameservers and instead use your own. You should also setup A Records for the nameservers, this will be done when you go through the Nameserver Setup section in WHM.

Final part would be under the Main WHM Configuration where you would change the default nameservers to use.

That should be it.