[pkovak]

There were several suggestions that the software should support Calibre. I won't tell you exactly this, but lets say our hypothetical eReader knows formats A,B,C and D. Your software knows formats A,B,C,D and E.
If I use your software to add another book in format A-D, no problem, simple copy (and yes, folders would be great, I think it's must have in large library most of interested people have). Now what if I have book in format E? Software knows my eReader don't understand it, so best solution is to ask me if I want to convert it to one of the other formats (Calibre converts mainly to epub, good choice seems to me from epub wiki, not personal experience). If I say yes, then it's converted and the result uploaded to eReader.

Another thing: some devices can't be used as mass storage device. Don't do this. I may have some reason to put that 100 MB video file in it, I can't use it in an eReader, but I can download it somewhere else. My device, my choice. Don't restrict download / upload to your software.
Oh, and manging several cards with books? Like in PCs, several logical drives, but with option to search everywhere with single search. People will understand this. If you take it far enough and you really add folders, you can have a search function that will work in folder user choose, if he does not want to search through 500 books, but only 10. But this same search function have to be able to search even through these 500 books. User's choice.