Yes, you can create a custom domain for your organization. If you would like your customers (and agents) to access your support portal using your own domain, you can point your default support URL yourcompany.appypiedesk.com to your own domain like support.yourcompany.com. More details and procedure for this provided is provided in the settings section,
That is, there is a three-level hierarchy. For adding the articles, there needs to be a category and an associated folder within that category