The way that I manage all the variables is that I know which choices actually matter on a narrative level and what they mean, what their consequences should be. Whether or not you made a sandwich during your breakfast with Asterion doesn't matter too much in the long run, but there's a little list of things that we're going to call back to frequently and all the way to the end.
I already know how these variables will affect the story. There is a logic to them, which is clear to the entire team but probably inscrutable to the readers.
Perhaps the more interesting question is "How to construct these choices and consequences", to which my answer would be:
Think of the world, its characters, its events, as having consistent logic throughout all of it. Things keep going when the readers aren't looking at them. People have their stories. The world has its logic -- and you set out to keep these things consistent, moving and evolving.
When you start from the ground up like that, it's easier to come up with manageable variables.