I really would not recommend bundling mathjax with ebooks, that is going to be pretty fragile, not to mention greatly increasing the size of the book.
You use a script tag with type text/x-mathjax-config for doing MathJax config. In it you have access to the MathJax object. Look at the example on the page I linked to earlier.
Last edited by kovidgoyal; 03-16-2016 at 01:36 AM.
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