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Adobe ADE are for the ePUB books with DRM sold from the Kobo store. Kobo also has a proprietary DRM for ePUB books. That is what you are using when you sync your reader with the desktop application or over WiFi. If you buy from Sony, the books also use Adobe DRM. Digital books from Barnes and Noble use Adobe DRM as well, but it is a different flavour and will not work on the Kobo.
The Kobo user guide is pretty good at explaining all of this--including explaining a bit about how to use Calibre for library management.
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