This is really a GAE question, not related to web2py. By default the indexes are set automatically when you run your app in dev environment depending on what queries you use. But you can do it manually to by editing the index.yaml (above the #AUTOGENERATED line). On the next deploy the indexes will be updated.
To disable the autogenerated indexes and test your index definitions, you can run your app locally with: dev_appserver.py --require_indexes Read this article for more details: https://developers.google.com/appengine/articles/indexselection
