As mentioned at [1], Google Apps does not support secondary domains for App Engine apps, however it’s supported for domain aliases. If your requirement is primary or secondary domain, the only solution will be to open a new Apps account for that secondary domain and migrate all the user data, which can be a bit challenging.
If you decide to do it, you can follow these steps:
- Rename secondary domain users to the primary domain (e.g. usera@secd -> usera@prid)
- Delete secondary domain, create and setup a new Apps account for secondary domain. Deleted secondary / alias domain become available for registration immediately. There is no 24 hours wait period as with primary domains.
- Migrate email data via [2] or GAMME. For Drive and Calendar migration use corresponding APIs or Marketplace apps. Group archives can’t be migrated. Settings will not be migrated too and have to be set manually or via API (where possible).
To minimize downtime and impact I recommend doing migration over weekend. If you have an annual commitment for the x number of users on your current Apps account, contact Apps support for assistance in reducing commitment after you perform migration to a new account and setup billing.
[1] - https://developers.google.com/appengine/docs/ssl
[2] - https://support.google.com/a/answer/6003169?hl=en