You can add stuff from SD to collections which you created on the internal memory and vice versa. This way you only have one collection of that type but have all books within the collection that you want. This means that some books from your SD card will be in a collection which you created on the reader. It's the same if you put one book multiple times into a collection. You will have this book in that collection as often as you have put it into it.
Kind of a bummer, but once you know how it works, you can get around
