I did it to add mathjax and templates
first open the file build-config.js in the ckeditor folder in the wysiwyg plugin
you will find a link like this : http://ckeditor.com/builder/c61d20c3a0bc54626f78b15bd091fb1c
it is the config page of ckeditor with the original qa config used in the plugin.
Without leaving this page, add the plugins you need, download ckeditor at the bottom and replace the orginal ckeditor folder with the new one