Watch all of the App Engine videos from 2008, specifically the following 
(yes, they pre-date Java support on App Engine, but most of the principles 
apply):
https://sites.google.com/site/io/building-scalable-web-applications-with-google-app-engine
https://sites.google.com/site/io/under-the-covers-of-the-google-app-engine-datastore
https://sites.google.com/site/io/working-with-google-app-engine-models

Then watch the 2009 
ones: http://www.google.com/events/io/2009/sessions.html#appengine
Particulary 
http://www.google.com/events/io/2009/sessions/BuildingScalableComplexApps.html 
and http://www.google.com/events/io/2009/sessions/SofterSideofSchemas.html

Then watch the 2010 
ones: http://www.google.com/events/io/2010/sessions.html#App%20Engine
Specifically:
http://www.google.com/events/io/2010/sessions/appstatsrpc-appengine.html
http://www.google.com/events/io/2010/sessions/high-throughput-data-pipelines-appengine.html

The information in  these videos is invaluable.

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