The Eco Reader supports sub folders. Essentially you put your ebooks in a folder structure of your choice (and subsequent sub folders) on your PC and copy them to the reader (or use Calibre to manage your ebook library). PDF reflow is supported by the Eco Reader btw.
I can't comment on the Kogan but some reviewers loved it, others didn't (battery life was meant to be well below the 10,000 pages advertised, more like 1,500). A BIG advantage the Eco Reader has over the Kogan is a user replaceable battery, the Eco Reader has a battery door on the back and runs a standard Nokia mobile phone battery (quick google would give you the model number). A second advantage of the Eco Reader as I mentioned before, you can install firmware of your choice, BeBook, Eco Reader, LBook or Astak to find the one that best suits you. I don't know how long Kogan will support their reader, unfortunately some of their past products got released without any subsequent updates (think back to their netbooks which are seen no more).