How to switch your Primary Domain with the Alias Domain that is pointed to it.
Note: you will need to re-setup email boxes after completed and all email will be lost. Also, if you use a dedicated IP address, your web site will be down for 1-2 days while the DNS updates. Most websites however use shared IP addresses which will not have this problem. You can determine this in the WEB OPTIONS section of your Control Panel. It will say either Shared IP or Dedicated IP.
Log in to Control Panel
Select Domain Info link in Domain Settings menu on the left.
Click the Delete icon in the Domain name field at the top of the page.
Confirm the deletion by clicking "Yes, I agree with the above".
Choose whether you would like to preserve the content of the domain's directory.
Add the NEW DOMAIN (which was previously the Alias)
Confirm by clicking "Yes, I agree with the additional charges".
Enter the domain alias.
Remember to re-setup the email boxes.