You can put gtk.css in there and it changes the colors of the style sheet. But my question: does there exist a way to target dark and light separately?
At the moment if I were to target certain elements, it would change them regardless of the dark/light style selected in gnome-control-center.
That does not exist. See Federico’s blog for a status report on the current state, and a description of how that could be done.
Please also note that gtk.css is a poor way to apply themes, it is only really useful for testing. Generally it is not possible to write one global CSS file that will apply correctly to every app.