You have three options at the moment, when it comes to a 'multi-tenant' app such as you describe:
You can have a single app that your customers add to their domains. Your app will have a single datastore, but you can use the Host header to determine which customer is accessing the app, and segregate the datastore entries based on that.
Easy to deploy and upgrade
Easy for customers to install
Users have to have Google accounts, not Apps accounts, to log in.
You can deploy a fresh app instance for each customer.
Harder to deploy and upgrade
More customer involvement required to install
Provides firm separation of data
Users can log in with their Apps credentials
You can work with Google to create a new Apps Marketplace app
All the benefits of point 1 and 2, above
Requires Google involvement
No certain release date yet
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