I separate things into chapters with a maximum of 15 pages each, most of the time a bit less.
Example: With my story, I have 6 chapters and only 35 pages started so far. I have five in the first chapter because it's more a a prolog. It connects to the second chapter that has two main choices in it, only 13 pages. Then those two main choices go to different chapters, with a note in the name of the title of the chapter such as 'MP1S1' in addition to the regular name, signifying 'Main Path 1, Section 1'.
Variables are unaffected by this transition from chapter to chapter, it's organized, and you can make it so people don't notice the transition from chapter to chapter when reading the story, and it doesn't rely on other sites.