You can tweak the configuration, or even give a complete configuration, using in-line configuration. This is explained in detail in the MathJax Documentation. There are many options that can be configured, e.g.: What input and output formats to use, What delimiters to use for in-line and display math, Whether to do automatic equation numbering, Whether to automatically break long equations, and much more. These are listed in the config/default.js file, and in the MathJax Documentation.