Why do I need to set up nameservers in WHM?

So I have nameservers configured on the registrar level (ns1.example.com, ns2.example.com). When I installed WHM it said I needed to specify name servers. I don't get why this is. I'm already pointing my name servers to the IP address of the WHM server. What does specifying them in WHM do? And, will I cause any problems by having both of these set up? Can I safely leave the nameservers blank in WHM? FYI, I'm going to be creating many accounts, but not in a typical reseller configuration. Thanks!