There's no need to decide right now the order of the cuts in the shot list, the editor will often decide that (with you, assuming you're the director).
By and large, that is the way it's done. But, if you are going to make the movie on the page, you visualize the sequence. Many of the best filmmakers do. Hitchcock drew every angle. He said the actual filmmaking part was tedious, because he already saw the movie on the page and had it in his head. Same with Spielberg, RAIDERS OF THE LOST ARK being a prime example.
I'm just writing down what I'm visualizing from the script. It helps me figure out elements, including FX, moves, and angles that I might otherwise forget, particularly cutaways - dog licking, clock ticking, toes on carpet - props, and backgrounds that I didn't even know I needed, until in the editing room, wishing I had extra shots.
The shotlist also helps plan scene transitions - getting IN and OUT of scenes, as well as connecting them. For example: In HIGHLANDER, there are several transitions between time periods. One shot shows a modern aquarium. The camera booms up, but it comes out of a lake, in the past. Two different shots with a seamless transition.
In EVIL DEAD 2, Ash swings his shovel and decapitates his girlfriend. Her head rolls right at the camera, blacking out the frame. Cut to shovel (which is also blacking out the frame), and gets pulled back.
I think animated movies are consistently strong, because of they are heavily storyboarded and pre-visualized.
I think of a shot list this way...
a piece of paper you can hand to someone else, and they can make a little check mark next to each shot as you get it. this way you can make sure you don't miss anything.
a bunch of edits on that piece of paper is going to make it a lot more confusing.
Yes, it is a checklist. Usually a set full of people, with all the actors in your face, asking questions, takes you out of the mindset of the shots and sequence. Despite all the distractions, you are able to just check the shots off.
Regarding a bunch of edits, I don't give a new number to shots that are the same setup. I either label them "SAME AS" or in a situation where there are several of the same angle, I may just write "M.C. of actors - intercut." The idea of "pre-edited" is visualization and is no different from storyboards. Put a bunch of frames on a paper and you have an edited sequence, even if it is rough.
And, finally, this can be just as important....
don't forget to shoot some impromptu shots whenever you need to.
If you get a good idea on the spot, go with it
This is the best of both worlds! This is where STAGECOACH wins the Oscar for cinematography, because John Ford decided to shoot during the thunderstorm.
The page is the guideline, but the location on the page is often different than the set or location I actually walk on to. If there is a bug or animal doing something interesting, I try to incorporate it.
My actors often stop and look at me, because I don't always say, "Cut!" I tell them, "Don't look at me. Stay in charactrer." That's because there are often scenes (especially basic sexual tension) where an actor an actress are "acting," but when they think the scene is over, they stop acting and sometimes say and do something totally natural, like a nervous laugh. I want the camera to stay rolling, when that happens.