You can define your primary domain through the CRM. First, login to your account. Then, click on my sites to enter the CRM. Next, click technical next to the website. Click on the domain in the menu and then click set main button to set it as the primary domain.
The primary domain is the domain name which you used while purchasing the server. The main control for your server will be under this domain name. But, the controls apply to the entire server, including any additional domain that you may have hosted on the server.