I am still working out how I manage all of my documents. I usually just open them up from the download\news folder where Calibre set up and then decide which one I want to add to the library. This is not as efficient but so much of what I read is a quick glance and then delete. Once the eDGe software improves I think Calibre can follow right along. On the Nook it works really well. If I add or delete anything on the PC the Nook just syncs up. Cable required of course.
The Calibre server via browser works well. Again if you have 10-15 items to move over it is pretty quick. If you are moving over a huge collection the cable route would make more sense. One thing I don't like on the eDGe is scrolling through the library. Seems like I always end up loading a doc that I didn't intend to because of the way I touch the screen to get it to scroll. Give me some simple Page Up and Page Down buttons on the LCD and that would be fine.
It would be nice for the auto-update stuff to let you choose which folders to auto add. I wouldn't want it to do everything. Newspapers that I read on a daily basis don't really need to go into my library. I glance at them and delete them. I would like the library to be able to read things from the SD Card so we would have the same features. Maybe I am missing something but I believe if you take something from your SD Card and add it to the Library the file(s) is actually copied to the internal storage.