Sorry to hear you are having problems but hopefully it will all become clear.
Assuming you have Reader Library open all you need to do to create a new collection is is click on the '+' symbol in the bottom left corner.
This will create a new collection named 'Untitled' which you can click on and rename to whatever you wish.
Click on 'Books' to view your library and you can then drag titles from there to your new collection. These collections can then be dragged and dropped into your reader.
To remove the collection just right click on the collection and select delete. This will only delete the 'collection' the books will still remain in your library and on your reader.
I hope this all makes sense, if not I'm sure someone else will be able to explain it all more clearly.