Yes, the only automated way that I know of to produce kepubs is using the calibre plugins. You can do it manually, but that is a lot of work.
If the books are not appearing in the library, there is another problem. dordale has some suggestions as to why. If they are OK, have you checked that the book is actually copied to the device? Does the processing screen get displayed when the device is disconnected? And does the progress go all the way across?
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