I don't, but I cheat. I have a notepad file with certain milestones of progress, accomplishments, and general goals to work toward, and what material I've included that work toward that. I don't PLAN that material, but I track it there. keeps me from re-reading my work constantly, and makes me have to remember things properly, or there will be an embarrassing mix-up.
But generally, my prequel was something I had floating in my head for so long (the base progression at least), that I never really had any worries about it. Just small details tied to it, which...again, I tracked.
It allows me to brainstorm how to flesh things out, and gives me a wide perspective of everything that's happening. Now that I'm on my Mass Effect arc, the game's done most of the work for me, so again, I get the fun of fleshing stuff out.
But usually, if I'm not working on something set like that (for instance, my ongoing World of Darkness campaign that I manage and my players determine), then I keep tabs on the key points of each chapter, jot them down, and then write new material. Eventually, I might need to check back on certain plot elements, but it's always nice having something of a cheatsheet handy for those cases, so I don't get caught entirely with my pants down. Helps me keep two sides of the story going at once: the framework (outline), and the canvas (the actual story)

Hope that helped? Slightly? Maybe not?