May not exactly same as your situation, but I'm running AEP and webapp on same gae application and share same model, by "version", described as item2 on following link. http://googleappengine.blogspot.com/2009/06/10-things-you-probably-didnt-know-about.html
for example: http://myappid.appspot.com : default version, aep code - define model in myapp.models as class MyEntity(db.Model): http://mywebapp.myappid.appspot.com: version "mywebapp", webapp code - define model as class myapp_myentity(db.Model):
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