I've just had the same result as Zreyl, where my overwrite folder only contained the TES5Edit Backups folder with the *.backup files. Thought I'd done something wrong too - for quite a while - until I found this thread. :) Maybe a short note to say "*some people have reported that their cleaned files are written directly to the /Skyrim/data folder". It's all a bit overwhelming if, like me, you have very little experience with modding and then a little detail like this can send you in circles for a long time
Thanks for the work, I'm finding STEP a great help!