One real key to writing an unruly, hard to organize text is transition sentences. There's no perfect path through a complex topic, and sometimes no very good path either. Put together an acceptable one and write great transitions.
@Sandra
Oh, but what if it's all of that? Fiction interwoven with exposition and instruction? I've been trying to write Traverser for seven years. There's no best path. There's pieces that add up to an understanding if you read them all.