You make up the rules
There's only one real rule... you have to use the footage! Why? Because you can't afford to shoot the whole episode, AND because so much of it is really terrific. After that one rule, you make the rest up.
I know you are all thinking that we do something magical to make it all work together. But the truth is that if you were sitting there with us in our meetings, and then sitting on my shoulder as I wrote, you would see that there's nothing revolutionary going on. In fact, sometimes it's hard to stay awake.
You look at the Japanese episode, you see what footage you can use. That footage is pulled out and put onto a separate file, so that you can easily look at it during the writing. Jackie and I kick around ideas, coming up with a few we like. I talk with Jonathan about them, we agree on a direction.
We write an outline. The outline includes the footage (which we underline to delineate it from footage we have to shoot) so that everyone who reads the outline can see our plan. The outline is shaped a bit by other opinions, and then we write it.
Jackie and I would review each other's work, and then pass it to others. The opinions come in. We would rarely toss a whole script (unless it came from an outside writer). We make adjustments, then go to the first draft.
As various departments read the story, then come up with practical concerns (too many locations, too many extras, etc), and the script is adjusted for a second draft. The final read through happens at the production meeting, where all the departments weigh in and discuss with the director what they are planning. After the meeting, the final tweaks are put into the script, are a week later we're shooting it.
It's a very logical process. No magic, just the shear will power of many people moving the train forward.