I work with a co-writer, so I'll come up with usually the bones of a story, then flesh it out with my co-writer. Then I'll do thumbnails to get an idea of art and pacing which usually leads to some rewrites and story massaging.
We spend quite a while hashing out the story at that point, trying to find tie-ins and some foreshadowing. When we're really on our game we try to plant some seeds that pay off by the end, but we're still pretty new to this.
So we "plan it out" really well before final art gets made, but before that there's lots of plan changing.