This was the question from a fresh Ph.D. Since I have never done so myself, I really shouldn't give any advice. On my second thought, since all papers are written the same way, at least for me, so I replied as follows.
Dear Alli,
I would suggest that you write an outline for each paper, including a list of figures for each outline. Then, talk to your adviser, to see how he feels.
I cannot write a paper without getting all the figures first. As written in my Blog, I write captions first, and think of a story line using these figures.