First off I will suggest against using mixed unless absolutely necessary. In most environments it's not a good thing.
That being said each file or directory will have either a set of UNIX permission bits or an Windows ACL. Any user (root included) will be mapped to the appropriate space according to the permissions on that file. This is why most people map root to a Windows Administrator account to make sure it works either way.
But I generally recommend choosing unix or ntfs for a security style if at all possible. Mixed mode is not required for multiprotocol access and picking one of the other two modes simplifies permission issues.
-- Adam Fox