Did you install this as the Easy one-click, or the Advanced? The Easy ones might not show up in your Manage Domains section. This section is also where you have the option to Show Hidden Subdomains, or leave them hidden.
Once you've installed/created a site on a subdomain, there's not much you can do to "rename" it as your main domain, but you can create a Mirror of your current installation:
Under Manage Domains, scroll down to plain old halphillips.org and click Edit in the Web Hosting column. On the new screen, scroll down to Mirrored and use the dropdown menu to have it mirror barbelith.halphillips.org and then click on the Mirror this Domain Now button.