Step by step workflow:
1.Get codecs. I used the cineform codecs that get automaticaly installed with the free cineform studio.
2.Create preset in Adobe Media Encoder. Here you will choose a format, video codec (cineform)and video settings. This preset will then be shown as a trasncode option in Prelude.
3.Transcode in Prelude. Ingest your media and click the “transfer to destination” option and the “transcode” option. Whithin the format of your preset you should find the preset that you created.
Thats it, Adobe Media Encoder should take it from there and you should have new files created in the specified folder.