First of all I would like to note that Q&A section is intended for Kentico community and we cannot guarantee a timely response. If you need help more promptly, please forward your questions to email@example.com.
Regarding your questions, to map a directory, it means to forward all media files to a certain S3 bucket on the storage which you can cpecify as it is described in the documentation you were referring to. However, it does not necessarily mean all current media files will be moved from your local file system to the storage. Unfortunately there is no automatic synchronization mechanism which would make it work. In fact only new files which you add to Media library will be automatically pushed to Amazon S3 after you configure Kentico to use this storage. If you wanted to push your existing files there as well, you can copy them to the respective bucket (e.g. via CloudBerry Explorer for Amazon S3) and regenerate the links by re-importing those files in Media libraries -> your library -> Files -> Selected files: Import.