<p>Since the Google App Engine Datastore is based on <a href="http://research.google.com/archive/bigtable.html" rel="noreferrer">Bigtable</a> and we know that's not a relational database, how do you design a <strong><em>database schema</em>/<em>data model</em></strong> for applications that use this type of database system?</p>

As GAE builds on how data is managed in Django there is a lot of info on how to address similar questions in the Django documentation (for example see
here
, scroll down to 'Your first model').
In short you design you db model as a regular object model and let GAE sort out all of the object-relational mappings.