Hi Daudi,
Creating hidden directories could get messier because, if Iliad creates a new directory for each PDF, the number of files/folders will be practically doubled. Yet, I think the benefits FAR outweigh the potential costs especially for those who have to manage 1000s of documents.
I use Endnote for managing my references. Endnotes also creates a directory for each PDF files linked to the software (and keep the PDFs in the respective directory). Now that I have an Iliad, I have to have Four different copies of the same documents in four different folders--two for Iliad (one for sync and the backup created by Companion software), One for Endnote, and one for the main collection. This not only wastes space on my hard drive (7GB x 4 = 28GB) but also requires a lot of my attention to manage them. It would have been much easier if I could simply sync my literature directory with Iliad.
Also, any further revision to my document collection/structure gets much more complicated. As I have to sync back and forth between Iliad and PC, this makes room for mistake and headache. I see there is a lot of room for improvement in Iliad's software (certainly for such an expensive piece of gadget). I hope the usability of the software gets better sometime in the near future. Otherwise, I may have to go back to my X60 Tablet and continue to destroy my eyes with the flickering screen
Thank you for your comments and suggestions.