This actually has a few different factions to it. There is the straightforward thinking about the linear plot. There is the thinking about the journey each important character takes. There's also the part where you need to come up with those little moments that foreshadow future events (events that may even be three or four books away).
And then there is this nebulous thinking where the novel as a whole sits and swirls in the mind without anything specific being focused upon. I envision this churning mass of something, almost like some cosmic soup, and I drift with it in my mind. Sometimes this simply fades into nothing but every once in a while part of the swirling mass will click into place into something solid.
This can lead to a clarification of a plot point I've been struggling with. Other times this can lead to a revelation that opens up an entirely new facet to the story.
And sometimes, like today, it reminds me that I really do need to purchase a whiteboard to visually lay out the plot.