One of the most useful tools for the analysis of complicated archaeological stratigraphy is the well-known “Harris Matrix,” developed by Edward Harris, and well-known through his important book:
Harris, E. C. 1989. Principles of Archaeological Stratigraphy. 2nd ed. London: Academic.
This method provided a very useful, logical, visual, and user friendly method in which to portray detailed archaeological stratigraphy, in a manner which can often assist crucially in understanding the sometimes quite baffleying stratigraphy of a site.
I was just informed (by Oren Ackerman, courtesy of Mary Larkum), that the book can be downloaded for free at the following site: http://www.harrismatrix.com/
Definitely worth checking out!