It's not at all well developed yet.

I've been using the Amazon web reader (mostly because I'm in Beijing at the moment and getting anything onto my kindle is a pain). I have the reader full-screen and Atom in Zen mode, and switch back and forth with i3.

For the books already there I took notes as I read. For the current book I'm trying out reading a chapter, writing down notes from memory and then skimming the chapter again to see if I missed anything.

For stuff I want to follow up I've been just putting TODO in the notes rather than breaking the flow.