As for the multiple bitrate HLS, you will do so by this example command:
createhlsstream localstreamnames=TVM_360p,TVM_480p,TVM_720p targetfolder=/var/evostreamms/media/TVShows/HLS/ groupname=TVM chunklength=10 playlisttype=appending
As you can see, you simply add the localstreamnames you put from pullStream to the localstreamnames parameter of the createHLSStream.
As for the "not stopping" creation of ts segment, this happens because by design EMS retries the session everytime the VOD is fully consumed i.e. When you pull a VOD, it consumes that and writes it to ts (as in your case), it does that until the VOD is fully consumed, however, when it’s done it reconnects again and consumes the same VOD from the start. To avoid this kind of behaviour, just add keepalive=0 in the pullstream parameter.
pullStream uri=rtmp://localhost/vod/mp4:TVShows/Blacklist_S03E07_720p_H264_AAC.MP4 keepalive=1 localstreamname=BlacklistS3E07_480p keepalive=0
This command will consume the VOD only once.