Current, detailed methodology for calculating the WCS score is not known outside of admissions. If you search enough you can find The Rand Report and other sources which provide some insight into how the score was calculated in the past.
What is known is that the breakdown remains unchanged: 60% Academic, 30% Leadership, and 10% Physical. Also, much of the input is purely objective: X points for a specific test score, Y points for Class President, Z points for Team Captain, Q points for Boys/Girls State, etc.
Because much of the tabulation is based on standardized check boxes, it is important to communicate on the application and to your Regional Commander any items that may not fit neatly into the standardized categories. The Regional Commander calculates the WCS score and can make judgement calls in such cases. The WCS score is verified by another Regional Commander to ensure accuracy and fairness.
This is for USMA. Other SA's may differ in some aspects, but are probably similar.