The way I would approach it if I was to make a VN, is this.
1. I start with the basic idea. Where it starts, the middle, and the end. These aren't very in-depth. They're just enough information to give me some references.
2. I then answer the 5 W's, Who, What, Where, When, Why and How. This is repeated for the middle and end sections.
3. I further break down the start, middle, and end into chapters. This allows me to concentrate on specific parts of the story without being overwhelmed by the overall story. Of course I'll occasionally check back to make sure the story is still coherent.
4. Make sure that my writing doesn't complicate the transition process over to whatever game engine I'm using. What I mean by this is, writing a story doesn't necessarily translate correctly into code. So not to make extra work, I write my stories in a way that takes the least amount of effort to transition into the appropriate game engine.
A quick example is, instead of writing "John wasn't fully aware that he took someone's undergarment" I would do this
*Image: John holding an undergarment*
John: You wanted to talk to me about something.
Suzy: You didn't have to steal those. I would of kindly handed them over to you.
*Image: John turns around, bring undergarment down, hands them over.*
John: Definitely didn't steal them.
In this way, when I take a break or whatever and come back to my writing I understand the structure of my story.
5. The coding phase. This is where I start implementing my variables and such. This goes back to #4. By reading my writing, I can easily determine if I need to do extra stuff or not, if not, I can pretty much just do a Copy/Paste where appropriate.
Mind you this is broad overview of my workflow. Don't take this at face value as there's many ways to approach this and the structure is different depending on the game engine used. The main takeaway is understand where your story starts, where the middle is and how it's going to end. From there it should give you a basic ideal of how you want to structure your story so that you can write it while maintaining a balance transition into the game engine of choice.