To me, writing is a very physical process. I lay out the entire book with the two narratives side by side on my bedroom floor, and just get down on my hands and knees and start looking at it in that physical space. "Does this really follow from this? Should this be here or elsewhere?" I will literally cut the paper into paragraphs. I'll cut it into segments and move the segments around from one narrative to the other until I feel that I've found the natural structure.