I guess that Shannen just laid out what was to happen in the scene, make sure everyone knew what to do and just went for it.
I found a picture of her directing The Good, The Bad and The Cursed and it looks like that's the kind of thing she did.
But have you ever noticed that the episode before the ones she directed Prue is conveniently out of the way.
*Apocalypse Not - Prue gets sucked into the astral plane.
*Bride and Gloom - Prue is unconcious for most of it.
*Look Who's Barking - Prue gets turned into a dog.
Think that was done so Shannen could sort out what was gonna happen with the ones she was directing. That or it was one major coincidence!
Shannen is very talented, she managed to juggle directing and acting very well.