Right now, my issue is that the nameservers I have created, don't really exist. The two hostnames ns1.mysite.com and ns2.mysite.com are not resolving. mysite.com, does, however resolve to the default apache directory.
All that means, is that apache is running, and that the IP is being pointed to directly from GoDaddy. I really think the issue lies within the correct settings in the GoDaddy manager.
I have tried using my domain name, my IP, and both nameserver domains as the nameserver choices for a second domain I have registered, and neither one is accepted by GoDaddy or Namecheap.
My thoughts were, it isn't an issue with either one of the registrars, but rather a setting I (you, and possibly others) have misconfigured. So, below is the setup of names I have working... hopefully it helps.
DNS Manager Settings
IP Address: xxx.xxx.xxx.xxx
Nameserver 1: ns1.mysite.com
Nameserver 2: ns2.mysite.com
ns1 and ns2 are both xxx.xxx.xxx.xxx
GoDaddy.com DNS Settings
Originally, before they added the DNS Manager, I had my IP's forwarded to, but now they allow the manager... and the settings are as follows.
@ and WWW are both xxx.xxx.xxx.xxx
That's essentially it. I just removed the few site examples I had been playing around with so that I could start from a clean slate. If anything above looks incorrect, please let me know... or if you need any conf files, etc, please reply. Hopefully this "problem," if it really is a problem, not just a misunderstanding (or lack of knowledge) can get resolved.