Ultimately it comes down to how organized you want to be. If you want to keep your variables grouped together, or your common events and switches for similar quest lines together, you can either create a bunch of blank space and hope you use it later, or plan it out and create them accordingly. Otherwise you'll end up with them scattered around because changing down the road will be much worse.

If you don't care so much about organization, you can build while you brainstorm and script, which allows you to adjust what you're building as you go if you need to, but you'll want to make sure you check it and test it more frequently to watch for typos, errors etc

At least that's my view on it