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I tend to try and write out a general outline of my plots in summary/synopsis style so I can have a loose roadmap for how I want the story to progress before I begin writing (though sometimes that ends up changing as I write just because of feeling things out).

When it comes to writing the script itself, I just focus on scratch writing until I get to the end and then work on editing and revising afterwards, once everything's done. Focusing on getting to the end rather than making sure everything is actually good-- editing comes later.

You said you had multiple endings in mind for your story. Is your problem trying to figure out how to get to the endings? Or trying to figure what those endings are? Visual novels don't need to have multiple endings-- my personal project has multiple but the project I'm working on for this doesn't. 

If it's the former problem you have, then it might work to try and think from a simple "cause and effect" mindset. If you have particular endings in mind, it can simply just be "what choice can the player make at what moment to diverge the route?" Endings don't need to have a complicated set up of multiple flags to be set, sometimes it can just be something as simple as a single decision that causes a "butterfly effect" scenario.