I've found this whole SDK overlay business a mess and very confusing. I've found this document
'The distribution of the AIR SDK with ASC 2.0 is for pure ActionScript development only. It should not be combined with an existing Flex SDK.
To support Flex application development with newer versions of the AIR SDK, an AIR SDK overlay distribution that does not include ASC 2.0 needs to be overlaid over the Flex SDK bundled with Flash Builder 4.7.'
So if you are doing pure AS3 development there is no longer any need to do any 'overlaying' of one SDK Folder onto another. You just need to get the latest AIR SDK with complier ( http://www.adobe.com/devnet/air/air-sdk-download.html )
You should then update the AIR SDK if using Flash Builder via ( http://helpx.adobe.com/flash-builder/kb/overlay-air-sdk-flash-builder.html ) (Note it still uses the term 'overlay' but you are not really overlaying but replacing).
Can someone from Adobe confirm please ?