By doing it through Dropbox, you don't need to download them all to your iPad until you are ready to read them. So you can put all the eBooks you might want to read on Dropbox and download when you are ready to read. So you can have the current book, the next book after than and the next book again. Then you'll still have plenty of books on Dropbox waiting for you.
I prefer this to the Calibre server method as this works very well outside of home. All you need is a hotspot with your phone or a WiFi connection. Simple really and much easier.
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