Thank you both, that clears up most of the confusion in my mind.
Bypassing Calibre and Nickel altogether is an intriguing option. To be clear johnnyb, this hidden folder method is intended for PDF's only?
I'm wondering if the Kobo Start Menu (KSM) always has to be navigated when the device is turned on. I use the Sleep Wake cover, and 99% of the time am going back to an EPUB, so when I turn on the device or wake from sleep, I'd like to avoid having to press "Launch Nickel" or whatever to reach the Kobo firmware all the time. Is that possible?
Also, for anyone looking for an overview of KOReader, there's this video:
https://www.youtube.com/watch?v=i2oSOeAnD10