First of all, I try to keep just one view controller on one storyboard. This reduces merge conflicts (two devs change the same file at the same time) and will prevent Xcode from performing badly if there are too many view controllers showing.
Then I put each storyboard (which only has one scene or view controller on it) with its matching view controller class.
When working on a project I'm finding it much easier to find files.
In the picture above I also have related prototype cell classes that exist on the storyboard in the same folder.
I first got this idea from an article on Medium.com. Check it out! It's one of my favorite articles I've ever read: https://medium.cobeisfresh.com/a-case-for-using-storyboards-on-ios-3bbe69efbdf4