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If you want to use Calibre to change covers etc then I think it's easier to send your ebooks directly to your Kobo from Calibre by using the "Send to Device" button which appears when you connect your Kobo to your computer using the USB cable.
For your library books (where you wouldn't be changing covers or removing DRM or anything) you can just drag and drop them directly from ADE without the Calibre step.
As you select which books you want to transfer to your Kobo you won't get any doubles unless you transfer them both from ADE and Calibre so you just need to decide which program you want to use for particular ebooks. Neither of these programs will transfer books unless you select them to be transferred to your device.
If you also sync your Kobo with the Kobo desktop you will get doubles of the books you have purchased from Kobo. Whenever I sync (which I never do unless there is an important update) I always remove my books from the "I'm Reading" section so that they don't transfer to my Kobo. As I have quite a lot of books this is very tedious and so that's why I rarely sync my Kobo.
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