I think maybe doing it as a somewhat object/goal-based topdown thing would work.
Like, pretend it's a wiki, you've got a 'missile ship' article. First thing it has is links to the articles on fire controls, active sensors, missile design, engines, basic shipbuilding, and then the article itself talks about ways to put those together into a functional missile boat, assuming that you understand the requisite articles it linked.
The active sensor article would link to the article on research and would discuss how active sensors function and how techs feed into it. Missile design would link missile engine design and whatnot as prerequisites, and so on and so forth.
Once you've got those all lined up, you could set up 'progression level' articles that link to relevant articles, which link back to the articles needed to understand those concepts, and if the reader already understands a concept they don't have to dig deeper.