I tend to manage my library manually, mostly using Calibre for its command line tools, and for that reason I personally find kepubify a worthy alternative. Not sure if you're a terminal user, but I wrote an alias named "tokobo" that sends an epub to my kobo as a kepub, tokobo is aliased to `kepubify -o /Volumes/KOBOeReader'
(that target path is for MacOs, for Linux it would be something like /media/$USER/KOBOeReader, and for Windows it'd be a drive letter, like E
. I then just run it at the terminal, something like this:
$ tokobo MyBook.epub
I've found the conversions to be perfect for my needs, but I'm not nearly as concerned about the details, such as custom CSS, perfect metadata, etc, as some people here.