For starters, you might take a look at DoDPI's Test Data Analysis document. The following description is from the AntiPolygraph.org Reading Room:

http://antipolygraph.org/documents/dodpi-test-data-analysis.pdf

"This 61-page document appears to be a collection of slides or overhead projections. It provides an overview of the physiological reactions that DoDPI deems relevant for scoring polygraph charts, explains the 7-point numerical scoring system, and provides specific information on scoring of the Zone Comparison Test (ZCT), Modified General Question Test (MGQT), and Peak of Tension (POT) polygraph formats. This document presupposes that the reader has a general understanding of "control" question "test" (CQT) polygraphy (regarding which see Chapter 3 of The Lie Behind the Lie Detector.)"

You'll also find some discussion of scoring methods in the following DoDPI report:

"Comparison of Utah and DoDPI Scoring Accuracy: Equating Veracity Decision Rule, Chart Rule, and Number of Data Channels Used." Senter, Stuart M.; Dollins, Andrew B.; Krapohl, Donald J. Final rept. Dec 1996-Mar 2000.

This document has not yet been formally added to AntiPolygraph.org, but you can download it here:

http://antipolygraph.org/documents/ADA382164.pdf

The American Polygraph Association quarterly journal, Polygraph, has also published numerous articles on polygraph chart scoring.