Here's a list of some useful writing resource links.
One Page Dungeon Contest - Single-page custom "dungeons" (rooms, locations, etc) with descriptions, drawings, and notes.
One Book Many Readings - A technical article on structure of CYOA's and relationship to computer science concepts such as graph theory, the intricacies of state machines, and branch mechanics.
How To Write A Gamebook - Mapping describes a planning method by which you draw a map of settings first, add notes, and then flesh out from there.
25 things you should know about story structure
Stakes and how to make choices matter - Karen Woodward's series on How To Write A CYOA is a bit outdated but still useful and detailed with many links of material after every article.
Standard patterns in choice based games - this article is what most use to describe the structure of a game.
Whimsical - Web/cloud app for graphically planning, organizing, and mapping out the pages and connections of your game. Syncs to google account cloud. No work lost. Free.
MyPaint - If you have a drawing tablet, this is software which allows infinite canvas so you can just draw and draw and draw and plan all you like out to infinity, and then you can get rid of paper clutter in real life.
Scapple - Basically a mindmap software that allows custom structure instead of branching from one central point. Has a free 30 day trial, then a one time payment if you want it.
Anyway, there's all sorts of stuff out there for writing CYOAs. I suppose I'll mention some of the more well known ones.
I've heard Inkle was dead, but I think it's still around in some form. ADRIFT is still alive, but just barely.
My old stomping grounds Infinite Story is somehow still alive too and even active enough to have stories posted on it from time to time. I suppose if you wanted to just mess around with simple engine it's worth a look. (Forums are long dead though and don't expect anyone regularly rating/commenting on stories there anymore.)
Infinite Story
I know Twine is very popular with at least one member here. (Try to guess which one!) I suppose if you were going for the mainstream "I want to potentially make some money" route (As opposed to y'know the based underground scene we have here), you might use it and put your creation on itchio.
Note I said potentially make some money, no guarantee you'll make a lot (or any!), but it's definitely a better set up than choicescript (Which is a rip off anyway) and becoming a CoGite slave sucking off Jason "Mega Cuck" Hill. Seriously, do not do this bad thing.
There is also Songbird which is a newer IF engine designed by the vagabond Cavus Rex. He's still looking for writers to use it as far as I know. Here's the thread if you want to know more information about and he's sometimes lurking about on here so you could ask him directly if you so desire.
Songbird Thread
And of course there's just using Google docs, forms and spreadsheets to organize things or even a regular pencil/pen and some paper if you're into the whole Boomer way of doing things. (Or your power went out and you're currently living in the dark ages.)