Create a Timeline
I like to come up with a way of measuring time, whether I'm going to use it in the story or not. Making a calendar as part of the world-building process is just something I find fun. It's not necessary, though, for the timeline. It's just as easy to use Day 1, Day 2, etc., or Day -1, Day -2, etc., for the scenes that happen before the beginning of the story (like flashbacks).
The next thing I do is start plotting the scenes on a timeline. I go by calendar months and days that I create. It doesn't matter what format is used to do this. Whatever makes it easier to reference when putting all the scenes together. If there are scenes that happen on the same day, I put those in chronological order. If two or more characters share a scene, I only add the scene from the POV character to the timeline (and I delete the scenes from other characters who share the scene so I don't get confused later).
Once I do this for each character, I add all the scenes for the main storyline into the manuscript folder in the timeline order. In Scrivener, I just move the entire "index card" into the manuscript folder. I don't worry about chapters or anything yet. That comes later. I leave any scenes that are subplots in the individual character's folders for the moment. If the scene doesn't drive the main storyline (like a love affair between two characters or any mission or adventure that has nothing to do with the main story), it's a subplot.