The global HEADER code injection (https://your-username.squarespace.com/config/settings/advanced/injection):

<!-- #1: Load MathJax-->
<script type="text/javascript"
   src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>

<!-- The following scripts only work AFTER the script that loads MathJax -->

<!-- #2: Enable equation numbers via \begin{equation}. -->
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
  TeX: { equationNumbers: { autoNumber: "AMS" } }
});
</script>

<!-- #3: Enable proper inline equation via $, and also process escape characters (e.g. \$). -->
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
  tex2jax: {inlineMath: [['$','$'], ['\\(','\\)']], processEscapes:true}
});
</script>

<!-- #4: Create a MathJax macro that reset's the equation auto-numbers. 
Thanks to https://github.com/mathjax/MathJax/issues/1294 -->
<script type="text/x-mathjax-config">
MathJax.InputJax.TeX.Definitions.Add({
        macros: {
          setCounter: "setCounter"
        }
      }, null, true);
      MathJax.InputJax.TeX.Parse.Augment({
        setCounter: function(name) {
          var num =  parseInt(this.GetArgument(name));
          MathJax.Extension["TeX/AMSmath"].number = num;
        }
      });
 </script>

The global FOOTER code injection (https://your-username.squarespace.com/config/settings/advanced/injection):

<!-- Re-typset page in case it is dynamic, per https://stackoverflow.com/questions/25839396/is-it-possible-to-use-mathjax-on-squarespace -->
<script> 
MathJax.Hub.Queue(["Typeset",MathJax.Hub]);
</script>

The "post blog entry" code injection (blog settings/advanced):

<!-- Reset equation counter after every blog entry -->
$\setCounter{0}$