So you want to use flow charts and graphs to tell a story? Good. Go right ahead. Tools don't make the master, practice does and it sounds like you have lots. Everyone does it different anyway.
Writers generally are mostly text based thinkers then visual, filmmakers are visual since their medium is visual. They make storyboards that help them see what they are planning on doing.
However, you can try something to practice on. Good look up monomyth aka Hero's Journey and enter that into you flowchart as the top level thing. Then you can break it down into how you are going to pull off each of those steps.
You'll want to create character sheets and setting sheets to round out your world.
The main thing is to write a story to completion and get it out there. Use the tools you know is fine.
There are plenty of article about how different authors did their work. The one thing every successful writer does is finish the story and put it out there.