Honestly, I'm not sure that I do. It feels like I do, as the deeper that I get into a complex system, the more clearly I can see the whole and how all of the parts interact.
But if I try to draw it? Usually I'll lose state and can't really picture it as well. I'd have to rebuild state as a graphic representation to do that.
So... I don't really know how my mind is organizing it, tbh.