I have never painted popper bodies that are bought. As I recall though they have a pretty hard surface. So I would think that a sharpie would not dry very good on that.....I think you are right about getting acrylic paint and coloring them that way! This is a fly that I have tied using foam glued together and then cut into a shape of a popper and you dont have to color them as they are already colored! I hope this helps!
I just painted it with sparkely nail polish..!