You can configure the encoder to generate streams through an RTMP connection to the packagers or in MPEG2TS format at a multicast IP address. To be compliant with the HDS protocol, the stream time should not go back in time. Therefore, you should configure the encoder to use Absolute time to avoid stream time getting reset on encoder restart while publishing the stream.
If you use multiple encoders, they must have identical configuration for the stream. Specifically, the encoding parameters including keyframe interval and bitrate must be same. They must generate identical timestamps for the same content. To achieve this, you should configure them to derive timestamps from a same LTC source.