The above sounds like a good system. What I do is keep the pupae in the fridge and hatch them out in batches in deli cups, with milk/pop/Gatorade lids to hold food (ground up cereal) and water so they last a while once hatched. Then I put the whole container in the freezer for a few minutes at feeding time so I can open the lid and grab out the desired number of flies for feeding. I also top up their water at this time if needed.
With food and water they last a few weeks after hatching.