You must set your account to know it is using the domain name. You can do so by going in to cpanel and adding it into either parked domains, or addon domains. Once you do that, your account may take up to 72 hours to propagate the domain.
mydomain.com was just an example. My actual domain is articles-and-tools.com, which if you do a whois lookup you will see that it is owned by Soroush (that's me).
If you just recently entered the domain, it has to propagate on the DNS. This may take up to 72 hours. You should still be able to access your site through the subdomain and IP.