SpamAssassin has three levels of configuration: standard, site-level, and user-level. Configuration settings at user-level override those at a site-level, and those at site-level override the standard configuration. Files associated with each of these setting levels are stored in different directories.
Rules and scores are the main elements of SpamAssassin mail filtering. These rules are specified in the files mentioned earlier. They use regex to filter terms or expressions that are typical of spam. Each rule is associated with a positive or negative score. Scores are used to filter spam from ham.