Overview of problem. Site was running on a Free version of Google Apps for over a year as a simple web page. We started developing it we deleted the old Google Apps and and migrated it to our primary App Engine account to avoid billing issues of two+ accounts. We couldn't get App Engine to recognize the Custom Domain even though it was in the Domains tab of our Google Apps Account. In searching I found Google limits using domains on App Engine (http://support.google.com/a/bin/answer.py?hl=en&answer=182081 scroll down to App Engine) I had to recreate a separate Google Apps account to verify ownership of the domain. Site is up and operational now outside of SSL. The issue is that when I go to https://admin.google.com/CPanelHome#DomainSettings/subtab=domains and type the app id to enable SSL on the domain Apps account it routes me to create an App Engine app instead of to billing. Because the app is running on the primary App Engine account not the Domain account.
It seems someone must have ran across this and solved it. How do I enable my primary Google Apps account to verify ownership of the domains and allow App Engine to use it? I have a lot of domains that will be hosted on App Engine and a lot of integration between the sites that would really need to be all under a single account to facilitate.
I noticed in searching that Google is offering a free year of Google Apps for customers using App Engine to host a application. Is Google expecting every domain to have a full Google Apps account and host on separate App Engine accounts? If so that would really limit our ability to use App Engine.