Your root website will not show up under Domains > List Domains; it will only appear under User Accounts > List Accounts. If you add domains to that user, they will show up under Domains > List Domains...
That first domain and in fact all domains associated with a new user will not appear under domains. The reason you cannot reach the domain is likely a port conflict with NGINIX. In my case when trying to use NGINIX two things happened. One, the domain was directed to /usr/local/apache/htdocs, so I received the default CWP banner page. And secondly, a website in the default location could not be reached. Due to this misconfiguration, I simply switched back to using Apache as my webserver and have no issues. In doing so, the default first user domain directed properly into the /home/USERNAME/public_html.
NGINIX setup and reverse proxies are difficult to manage by comparison to simple Apache in CWP. There are also a lot of bugs in the setup in addition to the setup being much more difficult.