Can you add some kind of queuing system for the worker bees? Or add mod support?
I'm not sure what you're after exactly, but you can modify some of the game's files by copying the json folder into your Hive Time user folder and editing them there.
I mean some sort of priority system for the where the worker bees use resources.
Upgraded production facilities let you control production priority sliders. Upgraded storage sells let you set minimum resource reserve levels that won't be used in production. These combined with the ability to pause and resume production for particular resources is as much control as I want to give players over resource consumption for production.