It’s like a middle-man, takes your typed ChoiceScript code and passes it to the engine underneath to produce an output like you would if you go through the node.js route. In fact, you can type all the CS code in a typical text editor (or any other code editing software like Atom or VSCode), and just open the text files using CSIDE, then run it.
The node.js route is relatively more hassle when CSIDE has a build-in way to run the code (show you the result), thus is my go-to recommendation for people unfamiliar with web development stuff and can install an executable file on their computer.
The relevant CS code (in text files) you will be editing or adding/deleting should be inside choicescript/web/mygame/scenes/ directory from your originally downloaded bundle, independent of the node.js part of the instruction. Once you are ready to share your game, these text files are the ones you upload to dashingdon (a fan-hosted service, not official), or if you want to host it elsewhere, feel free to ask on the forum by then for alternatives.
(Dashingdon: Free ChoiceScript Game Hosting)