Dawned on me where I saw the option - in MCEBuddy itself. I've enabled it - hopefully this means from now on, series recordings that are converted by MCEBuddy, will get automatically placed into subfolders based on the filename, which is ideal.
Edit: It works, but only drawback is it doesn't differentiate between series and other recording such as movies - so movies etc also get put in their own folder. Not perfect, but still more organized than everything dumped in a single folder.