" Just build stuff until it the pieces start to fall into place?"

That's exactly what I had to do. It's much easier to understand WHY certain parts of Flux were put in place once you start to use them in a larger app.

Deconstruct one of the Facebook examples (I'd recommend the todo app) and see how data is passed around. I had several light-bulb moments doing this.

Also: It helps to understand commonJS and a bit of node -- specifically what they use Browserify for.

I think reading through Flux framework documentations (marty's for instance) helps a lot. They do some abstracting on top and let you avoid some more in-depth questions about how to implement framework level features. They offer you some classes, and you just implement the classes to model the high level ideas of Flux.

I built a few small things and these examples really helped... https://github.com/facebook/flux/tree/master/examples/