I'm starting to think of projects now as a tree structure where the overall architecture of the system is the main trunk and from there you have the sub-modules, and eventually you get to implementations of functions and classes. The goal of the human in working with the coding agent is to have full editorial control of the main trunk and main sub-modules and delegate as much of the smaller branches as possible.
Sometimes you're still working out the higher-level architecture, too, and you can use the agent to prototype the smaller bits and pieces which will inform the decisions you make about how the higher-level stuff should operate.