Ok, let me see what I can do to help. In Godaddy, the nameserver fields are the fields where you tell the domain which nameservers are responsible for your domain. You need to point those to something.
You've got some options. Do you really want to run your own DNS? You could let Godaddy host the DNS for you. Then, add an A record to point your domain to your web server.
Bind is a great option. Are you using cPanel at all? One potential option for you, is use cPanel DNS Only. I run a 3 server DNS only cluster. Then, I have my hosting servers pointing to it. It's an efficient, geographically separated, fault tolerant DNS platform.
Let me know your thoughts, and I can help guide you further.