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I'd suggest only having one enabled. Either just have the basic Kobo Touch driver enabled OR the Extended driver depending on whether you want ePubs or kEpubs on your device.
Within whichever driver you can have enabled ensure that the shelf field is filled in with the calibre column(s) you want to use for the collections on the device.
If you are using a custom column then its name must be preceded via a # sign. If you use a built-in column then no # sign. That is why my example uses "#myshelves, series".
I use the #myshelves to allow me to tag books as belonging to (for instance) the Reference, Manuals or Cooking collections (or in fact multiple collections).
Using series also means books end up in a collection that is the series name as filled in on the book's metadata from calibre.
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