Thanks for asking this. I'm in the process of updating the Flagfox FAQ, and have just added a section for this:
Getting Flagfox working with Firefox sync would be far less problematic than it was with prior sync versions, but I chose not to dump things in there for the new version, as I think I'll need to write some sort of GUI/options to allow people to decide how to use it without screwing up their stuff. Sync support is on the perpetual todo list, and I may actually get around to doing it, one of these days...
For now, just copy the storage.js file as described in the FAQ. I think I will, however, shortly add the ability to at least import/merge from this file directly using the Flagfox options page. So, I'll add that on my (apparently never-ending) todo list, but higher up, as that's simpler and harder to mess up.