I ran into a really strange issue. I set up Collections and got it working but for some reason the Im_Reading column keeps duplicating itself whenever I click the book in device view. It seems harmless and it went away when I re-connected the Kobo. But now I'm curious what's going on.
Also manually adding a collection to already-uploaded books didnt seem to work. I re-uploaded the ones I'm not currently reading and then manually fixed the other ones on the Kobo itself.