I love, love, love both Ulysses and MindNode.
However for my current draft I'm using back to using Scrivener, which gave a free upgrade to Version 3 (Mac) a few months ago.
The new version of Scrivener allows you to tag your scenes with different colors that you define. I have different colors for OS, RS, MC, IC and Drivers. Then in corkboard mode, you can switch the view to "arrange by label" which is convenient for seeing how to arrange the different scenes and still visualizing the whole.