The transcode preset specifies the output format, codec and encoding settings that should be used when transcoding.
Reference frames are frames of a compressed video that are used to define future frames.
Some modern video encoding standards, such as H.264/AVC, allow the use of multiple reference frames.
This allows the video encoder to choose among more than one previously decoded frame on which to base each macroblock in the next frame. While the best frame for this purpose is usually the previous frame, the extra reference frames can improve compression efficiency and/or video quality.
Example below shows how to set 2 reference frames to the transcoder job;
<setting><key>num_reference_frames</key><value>2</value></setting>
That setting-line should be inserted your "TranscodePresetDocument".
More on different transcode presets and setup in the link;
http://apidoc.vidispine.com/latest/item/shape-tag.html#transcode-presets