It depends on your structure. If it's a linear VN, then you shouldn't need much more than a single Word file for your script with notations for sound effects, changes in expressions/ backgrounds etc. If you introduce items, exploration or different paths, then you'll need a map and consideration of what the effects will be of reaching the same path from different points where (for instance), the player might have different information available or triggered different events (I'm not an expert at otome, sorry, so I'm generalising a bit here!)
But if the focus is on relationships, you can always treat that as a kind of map and possibly split your dialogue into numbered sections with each number representing a different level in a relationship (on a separate sheet, you could have the key for these).
For the actual ideas, I find spider diagrams help. Just use your characters, or locations as centre points, and surround them with their characteristics. Sometimes this helps with linking ideas, or getting you to think maybe things could be better with a simple change. Going further, you could make timelines to help you know where a character is or how they're feeling at different points in time.
Be careful of going over the top with systems and things though. The hardest part of writing is always going to be the actual writing and too much organising and formatting can often just be a distraction- and if your work is scattered around numerous documents, then you'll find you need a new system to link everything together again! Definitely keep your master text file as clean as possible and only include what's strictly necessary.
As you say, though, every writer's different so only you know what's going to work best for you and your game. If there's one simple tip I'd suggest, it's using the bookmark and hyperlink tools. A good contents section can save you a lot of time in a complex story.