Umanna, It's my understanding that the thematic words should be entered in their encrypted form. Otherwise there would be no way of knowing the correct letter order for the jumbled down clues: 1, 4, 6. 7, 10, 14 and 17.
But I'm hardly an authority as I have little knwoledge of the thematic material and am struggling to finish the endgame. Am I right in thinking that the UNencoded version of the 9-letter thematic in line 10 begins with the letter S? If it doesn't, then I have been barking up a whole host of wrong trees.