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Calibre & ADE can both be used. My suggestion (not sure if it's necessary or not) but is to only upload to your Kobo from one program at a time - e.g. load books using Calibre, then eject device, let it refresh db; then do the same with ADE. This will avoid possible db conflicts.
Calibre & ADE by default use different folder systems. ADE has a weird bug in it (at least my copy does) where even if you delete a book from the software, it doesn't delete it from your hard drive. When you read & return a lot of library books this can add up - so I often go in and delete everything. So for this reason, it would be sensible to keep Calibre & ADE folders separate. Plus Calibre's default folder system is very nice (separate folders for authors, then books - similar to iTunes music folder)
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