KOReader should support PDF natively, as I recall. Dunno about KPVBooklet, but I suspect fw5.6.0 may have broken it --simply because it doesn't call upon gandalf.
One of the threads here, somewhere, is the font hack -- a wrapper for all kinds of goodness that is a superset of what you could do with USE_ALT_FONTS.
The font hack will install a KUAL extension for controlling itself easily.
Likewise, see our screensavers hack -- also controlled via a KUAL extension. (You will need to have Special Offers disabled the ethical way, by Amazon.)
The Kindle looks for supported ebook files in the documents folder
and all subfolders. This is totally normal.