Owncloud, Plex, Transmission and Encryption

I'm building my OwnCloud with Plex and Transmission. I want that all the Library of Plex and all the files from Transmission goes to some Shared Folder of Owncloud, for all Owncloud users can access it. I guess that is possible right? The thing is I want to activate the Owncloud Encryption is there anyway to that folder don't get encrypted or to be available for Plex/Transmission?
Thank you very much!

Are all the files on the same server? If yes, encryption adds a lot of complexity in the code of owncloud (which may fail, and often enough failed in the past), makes proper backups more tricky but doesn't offer real protection against an attacker.

I'm not really sure what you want to do? Do you mean the transmission torrent client? ownCloud allows you to use different type of external storage, where external means external to owncloud (it can be a local folder on the server, SMB, SFTP, ...). You can then share all files and folders on the ownCloud interface with other users (external storage as well if activated).