When you sign up for Google Apps, you give the name of the Internet domain for your organization. This domain name becomes the primary domain associated with your Google Apps account.
You can associate additional domain names with your Google Apps account, as separate domains or as domain aliases for your primary domain. However, at this time you can't change which domain is your primary domain.
Your only option for a new primary domain is to create a new account and migrate your data to the new account.