I had been using the sticky-note layout to try to work out the timeline, but there were too many things to keep track of, so I put together a spreadsheet to track event, year, section (I have sections and chapters, go tech writer, go!), and--here's the amazingly awesome part--subplot. If an event falls under a particular subplot, I flag it in that subplot's separate column. After that, I can go back and find out if the subplot makes sense or if I'm missing something. Boy, did I ever find some missing pieces that way.
The current two-sentence desc (this keeps changing):
Alien Blue is the story—literally—of aLet me know if you want a blank copy of the spreadsheet. It was handy :)
brewery owner who's been reluctantly hiding an illegal alien—literally—for the last sixteen years. The alien's pursuers have finally tracked him down, and have offered the bar owner a choice: wipe out everyone's memories with a mysterious brew called Alien Blue, or let them destroy the town. New Mexico