I may be the only person who feels this way about multi-pane editors, so please say so if I’m just crazy!
Problem: I’ve found that while using panes in Sublime Text (using Origami), I constantly set up panes (typically 2-up side-by-side) with the intent of using one pane for one thing, and another pane for another thing… say, CSS files in one and HTML in the other. Inevitably, I end up with files open in tabs across both panes, with little to no regard for the original intent I had for each pane. Worse, I may only end up living in one of the panes for hours at a time, practically forgetting I have another pane open despite it sitting right in front of me.
Possible solution: My suggestion would be enabling a way to create 2-up views of files quickly and easily, and to also quickly switch back to a single-file view on a whim. There’s an app that I think does this excellently already called XtraFinder, which adds (or rather, improves) tabbed views to Finder in OS X. To get a 2-up view of two directories, double-click on the tab that you would like to see display side-by-side with the currently active tab. This creates a sort of double-tab that has 2 panes inside of it (rather than panes containing the tabs, the tabs would contain the panes). Double-clicking the double-tab again will split the panes apart again.
IMO, this would be an excellent way to handle creating and destroying 2-up file views in an app like Atom!