I have been working on some major revisions of my novel Sanctuary (previously Tattooing Angels). It's kind of like a game of jenga in some ways, you pull something out and desperately hope the balance will settle. In other ways its like building a house, everything has to be supported, so if you're adding something in then you have to lay the foundations and then follow it through.
I recently decided the best way of plotting for someone who never plots was to print off a storyboard template (the kind people use to mock out films etc) and then put my chapters into each of the frames. Some frames are highlighted because they are action chapters, others are down time chapters to focus on characters and relationships. I then have to make sure that they balance out, that the reader isn't going from one mad action sequence to the next without being able to catch their breath, and they aren't getting bored waiting for something to happen.
The good thing about storyboarding is that when you want to add a new theme or storyline you can plot it through the novel, weaving it into the different chapters and watching its journey to make sure it works. You don't have to remember everything because its all laid out for you and you can tell where it would work.
You can download these templates from the internet, if you google 'storyboard templates' you will literally come up with hundreds of them and then its up to you to pick the right size, number of frames etc.
For a non-plotter like myself they are pure genius.