iNTiGOD

It wont have the horsepower for transcoding with emby.  Best bet is to store your media on helios and mount from nfs or smb to a more appropriate plex host. 
 
For perspective..The 4 core atom on my synology can barely keep up with transcoding on the fly 

@iNTiGOD which build / image version are running ? 
Maybe you can refer to the following blog post to check if the files on your system show to correct settings.