Generally, I write everything in plain-text, and then as a final processing step, bring it into Word and format it. I hit on this process when I was in college, since SVN, which I was using for version control at the time, is such shit with doc files. It doesn't help that it is absolutely miserable to try to add footnotes to a paper as you are writing it in Word, and at the time, and perhaps still, futzing with them was a good way to make Word crash and lose a few unsaved paragraphs.