The "ask my clarifying questions" can be incredibly useful. It often will ask me things I hadn't thought of that were relevant, and it often suggests very interesting features.

As for when/where to do it? You can experiment. I do it after step 1.

Before or after.

"Here is roughly what I want, ask me clarifying questions"

Now I pick and choose and have a good idea if my assumptions and the LLMs assumptions align.