I've installed KOReader in about 3 devices but I haven't yet cracked how to keep them all in sync - frankly, I don't know how the syncing process works.
I used to think that it syncs up both the books and the reading progress / metadata but when I tried doing it, it didn't seem to work that way. I would love to hear how folks have done this. It's about the only thing left that's keeping me from using KOReader more frequently on all my devices.
The progress sync is separate from how books get onto the various devices (at least as far as I know). Something OPDS capable works well to get the actual files across a network (or calibre via usb). For progress you can use their provided sync server or run your own (the original one gave me enough trouble to write my own implementation).