Manage In Place - is it possible to select a top-level and register all files regardless of subfolder?

We're lookng into Manage In Place and we can't find a way to register all files regardless of what sub-folder they reside in.   It seems to rely on document queues for actual registration, but does not have the ability to reach into sub-folders automatically. 

Are we missing something? Is there another way to achieve this?

Thank you,

Brian