Filling hollow blocks one level at a time
What's the phrase? "The perfect is the enemy of the good." 

Or something like that?

Is it better to pour them in one go? Sure. Is it enough better to make it worth a huge effort? Perhaps not, particularly if that's the way it's usually done by your laborers. The less time between pours, the better (i.e. one per day is far better than getting to it a month later.)

I would strongly encourage having "bond beams" (horizontal reinforcement) as well as vertical reinforcement. Depending on just how expensive concrete is in your area, it might be worth doing the reinforcement as a "post and beam" rather than filling every core hole. That does require blocking off the bottom of each bond beam where it runs over empty cores below. It gets you a strong framework with less material.