My inelegant solution was to have one copy of the book on my Kobo that had been added with ADE and another that was synced from the Kobo site. One could do the same with an ADE version and one sideloaded with Calibre.
I used one for reading the book, the other for reading the notes. I don't know if Kobo intends to build in support for multiple bookmarks, but it sure would be nice.
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