"Shelves" was the original name for "Collections". They were basically book shelves. But, as you can put books in more than one shelf on the device, collections makes more sense. But, they are really just a way to organise books together. How you do that is up to you. You create a collection, then you add a book to it.
"Series" are for books in a series. Such as the Harry Potter books. They have a series name, and there is a number for the order within the series. The series information has to come from elsewhere. Kobo populates it for books for books you buy from there. But, they do not read the series info from the book metadata. That can come from calibre when the device is connected, or using NickelSeries.
The information you read is a tutorial for how to create collections, and to a lesser extent, series on the device using calibre. The reason for this is that you can create collections on the device, but, it takes time. Doing it from calibre is a lot quicker. And most of the mentions of series is because before Kobo added the Series tab, using collections for series was popular.
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