I have a feeling that this is the problem: I believe that you've entered a full path in the WWMT UI... but in the WWMT UI you should only enter a relative path starting inside the models folder. You should only have a full path to the modelsrc folder in the global Wall Worm settings.
So, in the WWMT UI for the Model Path, enter something like just this: BIKEZ/rag . Doing this will export the QC/SMDs to the sdkcontent/modelsrc/BIKEZ/rag folder and the final compiled models will end up in the game's models/BIKEZ/rag folder.