soooooo im still new to writing longer works, but ive been getting a lot of method inspiration lately from A: (screen)writing youtubers and B: the anatomy of story by john truby. truby is a screenwriter himself and a lot of the references are for film, but its applicable to any storytelling. he talks you through writing an original story with loads of really great advice along the way - i really recommend buying it or finding it at a library.
in terms of my own method, i started the book / comic when i was 16 and it was like. autobiography hidden under 500 layers of separation, built from an older roleplay story id developed. so the development was really different to anything else id ever written or will ever write. i try to work a lot of time with lists and structures, but i find the best way i work is just intuitive - i spend a lot of time with the story in my head, sometimes hammering out lots of details with crazy-looking notes, and then just feel out scenes, worry about structure in the edit.
something i really enjoy doing is like... working backwards? mainly because im still developing so i always find myself digging out of my own holes. so i list out all the things i dont know, and all the things i do - i answer the questions, and ask 'why' about the things ive established. through like, half a books worth of notemaking, i manage to happen upon the answers.
something important to remember, especially when youre new, is that the story you end up writing will not be the story in your head. itll probably be better, but it might be worse. lots of creators spend their lifetime going over the same story in different ways trying to capture something about it theyve missed. but when youre new, the fact is youre probably gonna dig yourself some massive holes - youre gonna be halfway through and realise the story you want to tell is totally different because your tastes have developed, your knowledge of genre and storytelling and yourself has developed. you can start again, but i recommend pushing through, carving something you like out of whatever situation you stick yourself into. you can always edit, you can always reboot, years from now if you want
always remember: prefect is the enemy of finished. go for finished, that is hurdle number one.