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Based upon how you organise your books, KOReader is your best option. You would simply connect the Kobo to your computer via USB, then copy the folder containing all of your books on to the Kobo. It is a single operation, regardless of how you organised your books in that folder. The KOReader file manager will allow you to navigate through folders and sub-folders much as you would on your computer.
In my opinion, the KOReader user interface is nowhere near as confusing as calibre. Most people will only ever work with the file manager and reader modes. The functions are available via a menu on the top of the screen or a panel on the bottom of the screen. If you're using a small number of features, you should be able to memorise where the stuff you need is. If you're using a lot of the program's functionality, it can be overwhelming. It is also worth mentioning that the developers are open to improving the user interface.
Installing KOReader is tricky, but it is a one time thing. You can update KOReader via a menu item in KOReader.
One caveat: I don't think the current release of KOReader supports the colour Kobo models, but I suspect that the next release will. (I am using a development version of KOReader on my Libra Colour, and everything seems to work.)
To muddy the waters: I believe that Plato also supports CBZ files. It will allow you to organise books in folders, though it does not work like a traditional file manager. It has a much more elegant user interface. I don't know if it supports, or if it ever will support, colour models.
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