Sounds pretty good to me, it allowed the DNS to work at least
Did you end up using your own nameserver for your site with the same domain? Even though it's supposed to be impossible...
ns1.mydomain.com is the nameserver for domain.com
(within godaddy's DNS settings)
And one other thing, what do you mean by co-domain? Do you mean actual "sites" from the ISP manager, or just two A records for one added domain (ns1 and ns2)? OR, did you create domain1.com, domain2.com, and then assign domain2.com the two nameservers from domain1.com with both godaddy and ISPConfig?
I'm still confused, and this is making me feel like an idiot...
Edit: Ok, does the first actual site you create become the main site (ie. the server IP's actual website)? Because the first site I created is showing up as the domain I plugged ns1 and ns2 into... I guess I need a third domain to test it.