When you use dropbox, od a double check and make sure your files transfered. I received a message that they had but noticed I was missing 2/3 of my books. I looked at the folder in dropbox and many of them had a blue symbol instead of a green check. I reopened Calibre and saved to dropbox again and this time all was well.
I am keeping all of my books on my iPad. I have 64 GB of space and a WiFi model. By having them all on the device, I can make sure that I have what I want, when I want it. Call me silly, but I have the space so why not?
I am looking forward to folders though.