I wrote here the other day about how you can use Ulysses to read and edit non-consecutive scenes. Here’s an illustration of that in action from the book I’m writing now, the third in the Pieter Vos series (with you some time in 2016).
This is about halfway through the book when we’re heading for two different climaxes to a pair of story threads. They need to resolve issues raised in earlier scenes separated from the climax scenes by other action. It is much, much easier to deal with these though as if they were written consecutively.
So all I do is use Command-Click to choose the connecting scenes I want and that’s what I get — just the scenes I need. It’s a really efficient way to deal with what otherwise might be a complex task, and I also often find myself improving (hopefully) the earlier scenes I’ve written along the way.