Addendum with in-built chapters; Wizzy's advice is generally good, BUT if you have a particularly very long story (think of 50k plus) with lots of variable work and multiple chapters, then I found it easier to sort pages in these in-built chapters (pages are easier to find and it's easier for you to navigate and fix bugs).
There are sadly not many other ways to organize pages otherwise.
MORE TIPS
-1)make your own reference sheets for names of characters, important places, local currencies and every small detail you might need in your story. The size of the sheet really doesn't have to be big or a big time sink. Everytime you think it's a detail that it's important and you'll surely forget later, write it down somewhere. It will save you lots of time when you forget the last name of a character and have to go back and search through all of your previously written work to find that stupid detail.
-2)Keep the scope of your first story small, mainly for the sake of your own sanity. The story will balloon out of control otherwise. It doesn't have to chronicle an entire 5 year war, it can also be one battle. In regular fiction, I would say that it's entirely possible to write an entire story without an outline, but it would be a hard nope on interactive fiction.
-2.5)That outline will be your life savior. It can help you limit the scope of your story, iron out plot holes, determine climaxes and build ups or spot other inconsistencies and best of all; major story changes can be easily fixed at this stage. Want to make a new route, but you need something in the beginning to be changed? Easy peasy with little pain. Fail faster! (I've written multiple outlines of potential stories that I ended up not liking haha)
-3) keep in mind that you're writing an interactive fiction. Most readers won't see even half of the stuff you've written when they finish one of your paths while you're writing thrice the amount of a regular story. Make sure that every path feels as satisfying to read as any other. Play around with structures, delayed choices etc, take advantage of the fact that it's interactive. (Same goal achieved in different ways, supervillain route, other ways to develop your character etc)
-4)keep yourself motivated by splitting your goal in multiple small easily attainable chunks. Instead of: "fuck, I'm not even half way done with my story", you'll be thinking: "wow, I almost finished my third chapter, hurrah". It makes everything a lot more enjoyable.
5) Read other stories, preferably the ones on the top 100 to see what's the overall standard of the site. Also read some bad ones with a very low score. Compare them, see what works and what doesn't. I would recommend the Homo Perfectus series on this site. It's also a superhero story with multiple parts. It's a rather interesting case study, because you could see the author slowly improving with each consecutive part.