Anki's bundled MathJax support is loaded before your card content, so if you wish to customize MathJax, you will need to do so in the following way in your card template:
<script>
MathJax.Hub.Config({
...
});
MathJax.Hub.Configured();
</script>
Notes:
- Please avoid changing the standard open/close tags (
\(and\[), as Anki expects them to look like that.