Sticky notes!
No, really. Granted, the first draft of Swift as Steel was completely pantsed; I had a vague idea of what was going on, but a lot of things were developed on the fly. When I sat down to do the rewrite, I went through and put every scene onto a Post-It, along with what chapter number it was in. They were color-coded; I decided that if there were too many secondary colors in between Major Plot Point scenes, then something in there needed to be cut/condensed.
I rearranged post-its. I renumbered chapters. I deleted scenes, combined some together, and added a couple new ones. And then I taped them down onto a piece of notebook paper in order, putting down my new chapter numbers as I wrote. (My early chapters were way too short. I dropped from 33 to 20, and that's with a second draft that's fewer than 10,000 words shorter than the first.)
So, first make a list of major plot points and/or scenes that you want to write. Take a few days to do it, as you'll remember and/or think of new things as you putter around your daily life. Then sit down and put them onto sticky notes and start to arrange them in some semblance of order. Expect things to change as you go; that's why they're on sticky notes and not inked in blood on a stone tablet.
Use special post-its for your clever lines. Figure out where kind of where you want them (but be prepared for your characters to have minds of their own). Structure out your magic and figure out how to divvy up the exposition of how it works without loading too much into a single chapter. Use an entire wall for sticky notes if you have to!
I <3 sticky notes.