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Hi Tan, Kobo Desktop is a sofrware that runs on your computer, not on the ereader.
The ereader comes already set up with its own software. When you first register your ereader after a factory reset (i.e. when you put in your login credentials), you have the chance to set up the reader wirelessly, instead of using kobo desktop. This is needed for instance to update the software on your device, which again has nothing to do with Kobo desktop.
Once you have completed the first setup, to put books from your computer on your book via Calibre, you simply run Calibre, connect your ereader to your computer, wait for Calibre to recognise your device, and then transfer the books.
The above assumes that your ebooks are not protected with DRM. In case they are, then Calibre cannot open them, though you can still use it to transfer books (but you must authorise your ereader first, using Adobe Digital Editions).
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