I&W over or under paper for vent/chimney

I've read to put Ice & Water (I&W) shield around all protrusions, which makes sense, might as well seal up the nails. What I'm not sure of is do you put it down before the paper, on top after you paper, or is it just a preference?

Seems like you'd do Eves, then rakes/valleys, the protrusions and then paper?