We are using AEM with Amazon S3. We are having issues upgrading instance of 6.2 to 6.3.
The issue we faced was we had few binaries were getting stored in CQ datastore and few were in s3.
What is the right configuration? Should we have all our binaries in s3? and it shouldn't store anything in Datastore?
Here is the AEM docs on this subject --
See the section on Amazon S3.
Hope this helps.