I do loads of my pre-writing physically.
I write little notes like you do and arrange them, and I also write loads of lists.
I keep track of all my lore and character specifics in little notebooks...

Lists are my main jam. I use a lot of bullet points and diagrams.
One of the things I do is draw time lines and pin point chronology on them (eg. when a specific important event happened or when a character was born) to get a broader perspective. Literally just... a line from the top of a page to the bottom with loads of offshoots on it.

I actually started doing the same process as you lately after I just try to wing it.
But after doing it and know all the plot point, I write a full script. then rewrite and rewrite.

I recommend reading this book. changed my view on story telling completely:

Google Spreedsheet; don't lose my work to HD failures. This might be a bit of a mess to explain so here's a blank copy of my file3 with a few notes here and there.

I try to focus less on events when making plot points and more on how it affects the characters. It gives me wiggle room if I come up with a better idea for how I want a conflict/confrontation to go down and I don't feel restricted to an event or feel forced to change a characters motivations/personality for a specific event to happen. Plus, with the spreedsheets I can drag plotpoints/events around and see where they fall in the timeline; beginning top and bottom closer to the end. There's other tracking on there too, like character/enviroment/object design and such so... hope it's helpful in some way.

i have an "overarching plot" bullet point list that has the general ideas for chapters
1

i rarely edit this but i move stuff around if i need to

i then outline my chapters and figure out the flow, i have up to chapter 8 finished

after that i script and draw it

I write down events that will happen in the future, but not in a chronological order. Then I pick one I think it's good and try to link it with another event that will happen next, both have to make sense

I also draw some scenes first to see if I can do that event, otherwise I put it on hold to find a better way to draw it, or I just delete it if I find too complicated/nonsense

I create a timeline and use Evernote to write down literally ANYTHING that’s on my mind. I later piece together the plot points and put it on my timeline.

I don't think I have the right to answer this, because I don't really have a process. I just play it out as I write.

From my "Storytelling Tips" journal on DeviantArt:

"Write down every new idea you come up with ASAP. Even if it's just a few lines of dialogue; if you like it, write it down somewhere. Later on you can go back to those notes and sift through them; see what's good, what's actually garbage, and what just needs a little work.
Furthermore, re-read everything often. In my experience, lines that I don't want to re-read are usually parts of the story that I don't actually like. Eventually, they get written out, no matter how much I thought I needed them before. I believe that an author should want to read every single word of their story. After all, if you don't want to, how can you expect someone else to want to?

[EDIT: This^ can get pretty lengthy. Sometimes your ideas will outweigh the actual story you have written, but that's okay. To put it in perspective, for Deadeye I have 82 Word-doc pages of written material. 1 page is the story arc outline. 5 pages are character profiles. 34 pages are actual chronologically-ordered comic scripts. The rest is just pure ideas~.]"

This is pretty much what I do, ^^ (Deadeye's Word doc is over 100 pages now, though XD). I have one Word doc for each of my comics and novels, sometimes I make separate docs for character profiles if they get lengthy. The point is to get all the ideas down and THEN organize them.

My steps:

• pre-write script
• go back and edit
• add a bunch of little notes for further polishing
• jot down ideas on notes
• implement them
• edit

I actually write the end first... Well, Characters -> Main Character/characters in a scene -> Beginning of Story -> End of Story.

This helps me out with plotting the middle pieces. I know where the MC will end up, and I'm just left to watch how they'll get there. When I write, I'm just pausing a scene that's playing in my head and writing down everything that happens as I watch it.

I do hit stumps sometimes, but I've found that writing later scenes than the chapter I'm currently working on always brings me back to being extremely motivated to write the current chapter. It makes me excited for the future scenes to play out, and makes me want to understand just what happened to get my characters into each predicament in the first place. I don't really "plan" with short blurbs often. I just write scenes and fill in the middle ground.

I also learned that whenever I hit major writing blocks, they get solved over time. This probably isn't a great way to go about it for nearly anyone else, but I work in a world I've been creating for almost eight years with my friend. We're still learning more about it every day. And sometimes I'll learn things that intertwine events and characters that I never thought would know one another, or that I didn't know existed when I was creating the original work. This has happened multiple times during my creative process, and my current story wouldn't be heading the direction it is without the introduction of a character named Senris Ny'Asa.
Senris exists because I started a new novel for a writing group. But he changed the entire second and third parts of my current work, and I was having the worst time sitting down and writing Part Two. (As in, I wasn't trying at all.) Now I know the entirety of Part Two and where it's headed, and I have the entire premise of Part Three ready to go. I just need to figure out the scenes I want to fit into it.

Other than that...

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I'm really

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Messy

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I draft and write over and over. I really only do about two edits in the end. But I find myself saving copies of my work when I change a word or sentence. Just in case it reads weird while I shuffle through, that way I can check my first choice and see where I was coming from originally. And I pile and pile the drafts, which all make one, long, shitty first draft.

But, I will say you should always have an end to your story planned out. If you don't, it'll go haywire and you'll more than likely lose control and motivation, because there's nothing your work is leading up to. One thing that all good stories have in common is that they end. The only thing that continues is the world, and the reader's imagination. And the ending of a story sets those satisfied gears to work. And that's what sparks inspiration.

I mostly don't plan a head much unless I've got a coherent idea for a story, I try to let it roll out organically.
I also do thumbnail not a script, because it's easier to do then to write a description of a image that popped to your head.
After that I write the basic text and dialog.
Just do what feel more comfortable and helpful to yourself.

@stnmaren What you do is quite similar to what I do now. I've gone through a lot of iterations of planning methods to get here, too haha!
I used to do sticky notes, word webs, excel sheets...

In the end, I now structure my stuff by bullet point based on story arc and chapter. However, by this point, I've already established the entire arc of the story and identified its main beats (which I call acts [not necessarily the way we normally use acts])

EG.

Act 1
(What I want to happen in this act)
Ch1
- point 1
- point 2
Ch 2
- point 1
- point 2

Act 2
etc.

I find breaking the story down by beat, really helps. As well as starting big, and going smaller. Not to mention all of this suffers regular revision!

The way I work on story nowadays is heavily built on what I've learnt from Story by Robert Mckee as @ramiek has pointed out. It is a FANASTIC book and even though it's about Screenwriting, almost everything applies to comics because we're closer to film than we are novels in terms of a medium.

That said it's a huge book but I just finished a summary on Story structure as explained by McKee here: Tips on Fundamental Story Structure3 . I use an understanding of this as a basis for organizing the gist of the story when I plot the outline.

Technically I use handwritten notes and then the index cards on Scrivener to organize my thoughts

But the actual mental process always circles around a few questions I ask myself after I come up with an initial premise or idea:

• If I were this character in this situation what would I do? (Ask this for every character cause it's their actions, often, that drive the story, even in reaction to stuff out of their control like a natural disaster.)

• What does the Character want? Why? What are they willing to do to get it? What happens when what they do doesn't give them the result they want? What are the consequences of that? And then what are they willing to do then, given those consequences? And so on.

• What are the Story values that oscillates back and forth and motivates the plot? (Eg. Life/Death, Victory/Defeat, Bravery/Cowardice)

• Does the end of a scene or act or even the story show a meaningful change from the beginning? Something that affects the protagonist?

I'm in the middle of writing out /aallll/ the plot I have with my writer. He's the brains but I have to physically record it because he's going blind. I might even try the way you have it with sticky notes, it looks like it would be much easier to visualize the story this way for myself. Right now we've just got a text document where I've got down the overall story theme and major 3 world events, then breaking it down and down into more detail in other segments.