Ok, I have done that, I created a sample site and put in those settings.
Mysite2 has the nameservers ns1.mysite.com and ns2.mysite.com (within ISPConfig), however, GoDaddy won't allow this. It gives me the "Unavailable error in field Host name" message, which seems to mean that the nameserver doesn't exist... but, again, with MySite1, GoDaddy is correctly pointing ns1 and ns2 to MySite1's IP address, and they both resolve correctly when browsing to them.
Within GoDaddy, for Mysite2, I'm assuming I should be putting in ns1.mysite.com, and ns2... as the nameservers, because if I have to point MySite2 to my actual server IP, then it will be doing the same thing as MySite1, and will become an identical clone, but with a different URL.
Thanks for your help so far, I appreciate it greatly