Check out the alpha plugin in the Developer forum if you're uninterested in Kobo store guff and Reading Life awards malarkey.
If you're used to working with Calibre, you're already way ahead of the game. I choose to do epub-epub conversions to strip line spacing/margin/font/etc pre-sets; your mileage may vary. You can manage your shelves with Calibre, too - there are detailed instructions in the stickies.
Lastly in fidgeting, you can upload your own fonts if you're not satisfied with the built-in ones. Make sure they're named properly, then just drag n drop into a folder called "fonts" in the Kobo (you'll need to create this; name it exactly.)
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