You'd issue an intention (order), the various commanding elements would trickle their instructions down to lower levels, and the results would eventually bounce back up, along with confidence and efficiency assessments. If you like, "we'd do it better if we also did X" which would be reviewed and implemented as necessary -- that would bounce around, until optimal achievable options are presented upwards, and so on. It's then a matter of deciding whether the player sees these distilled options, or the game just implements the best confident option, based on how much management you want the player to do. I expect at least some decision-making, just for fun.
So you can issue very general objective if you like. e.g. in order of increasing generality you might do one of:
- 'Research smelting level 4',
- 'upgrade the ability to extract iron from ores',
- 'research manufacturing',
- 'exploit your market', or
- 'find a new location and exploit it' for the most highly-skilled NPCs