It doesn't seem possible ATM to bind an App Engine application on a Google Apps Secondary Domain (sounds like a bug).
But it works fine on Google Apps Domain Alias.
- Go to https://www.google.com/a/cpanel/yourprimarydomain.com/DomainSettingsDomains
- Click Add a domain alias or a domain
- Select Add a domain alias of yourprimarydomain.com
- Follow instructions to verify your domain
- Go to your App Engine application dashboard
- Go to Application Settings
- Click Add Domain
- Type the domain name of your primary Google Apps domain (not the alias)
- Click Add new URL
- Select your domain alias from the dropdown list
- Click Add
- You will be asked to add a CNAME to ghs.google.com in your DNS configuration
That should work.