Well you're in the wrong sub-forum (this is for the tablets that Kobo produced for short time), you want to be just in the Kobo e-reader forum rather than going one step deeper to this one.
But to answer your question, you can put them directly in the main directory of the Kobo or create your own sub-directory for organization (realize that these WON'T show up in the device interface when you're reading). The only place NOT to put them is any directory that starts with a period ("."). They are hidden from the firmware. And yes it can handle comic formats. Do a search in the main Kobo forum if you need details.
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