[Morf]

...I can add them to a collection but then I have them twice on my kindle...

It's important to realise that collections are not folders, they are more like tags. So you don't put a book into a single collection, you can add it to one or more collections - for instance a book may be in "classics", "scifi" and "unread" for instance. This is why it feels like a book is on the Kindle twice - if your home page list is sorted by author (say) it will appear there and also within the collections.

This is why it's important to use "Sort By Collections" as Susan suggests.