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Are you trying to setup ns1.yourdomain.com and ns2.yourdomain.com? If yes, you CAN do that on GoDaddy ... I just did it the other day. You just need a dedicated IP address to point each of those name servers to, which your host will provide you with. They must go to a DNS server though and not just your box.
If you have that, hit me up on ICQ and I'll walk you through it.
The most important thing is that it must be pointing to a DNS server.
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