There's a few programs for writers that I know organize stuff for you all within them - Scriver I believe being known to be one of the best.
Personally I just do it the super old fashioned way : make a folder on my computer labeled story name and dump shit in it. I do eventually sort it out into a few folders and make a few "master" files: calendar year if it's different than ours (starting in jan, ending in dec and such), a random facts list, timeline (backstory and instory as 2 seperate spreadsheet files) goes into it's own folder, images of character refs is it's own folder, and files specifically edited and meant for physical printing are in their own folder (along with the files for the covers). Some more detailed stuff like world building details are kept in hidden files on my website that I have access to, when I remember wtf I named the urls lol And others are in a "world" doc file...
I'm kind of all over, but it's ALLLLL in my "text" / "Novel" / "story title here" folders... If it's not in one, it'll be the root folder... Probably.