We're currently looking at this and debating it internally. I'm personally not a big fan of split-screen interfaces, partially because you already have a limited viewing area, and splitting it makes it even smaller. That being said, I'm not sure what we'll end up with.
Our first attempt at comparing verses (the Compare Versions feature) is one possible way to solve the issues. Another is the inline approach like we take with notes. Again, I'm not a fan of putting footnotes at the bottom of the screen, in a popup window, or in a split screen, because it's distracting to an extent. That's why we've taken the inline approach, with the ability to toggle them on and off. I kind of like how that works, but I'm open to your opinions on the matter.
We're working hard to on an interface that'll handle contextually linked content, and when we're happy with it, you'll see it appear (hopefully in the next version.)