I thought that ZUN wrote the mangas. Or was I mistaken?
He writes the manga in name, but leaves it to the artists a lot, as well. His involvement varies.
In SSiB I don't think he had much oversight. He just hit on important plot points and script, but with not very much detail, and left Aki Eda to her own devices otherwise. Inaba x Inaba is essentially just ascended fanon with ZUN's blessing. Since that one is just a gag comic there isn't as much need to exercise control. I want to say he also trusted Makoto Hirasaka with a lot, giving him more control over what the fairies do and just giving him basic plots to work with.
In WaHH and FS I feel like he retained much greater control. This is based on something either of their artists said, something about ZUN being pretty controlling with certain panels and the expressions in them. I'm almost certain he writes a larger portion of the script than he ever has and details more of what should be done, though still with input from the artists (see the heavy use of males in FS, which I'm almost certain is something Harukawa wanted to do).
In essence, I think he does manga the way he does the fighting games, entrusting a lot to Tasofro/the manga artists based on his basic scripts and plots. If they go too far off track on review then he dials it back or nixes what he doesn't like, which goes on until they reach the final product.