I think you could describe the structure as being a directed graph with labelled edges and stuff inside each node. You build it up by inspection, debugging, documentation (when it's around), experimentation. You know who calls x. You know what x does. You know what x touches. You know who else touches those things too. What does that one do? Hrm. gasp (literally). There's the race! :) "He fixes radios by thinking!"

But again the graph idea is a formalization. It's more fuzzy and messy in my head. The graph is not perfect and requires care and feeding to stay alive. And you don't actually see the whole thing at once. You can move around inside it but there is a focus. It's something your subconscious operates on as much as your conscious mind. And it's the subconscious that generates the intuitive flashes.