I am helping a friend build a wordpress site using a purchased custom theme as his parent theme. There is also a child theme.
We have tried putting it in the index.php (most logical source to me, since that's to me that makes the most sense, but obviously WordPress works differently).
So all I am trying to figure out is, where in wordpress do you put the script tag (where you put code, not referencing jQuery we already have that)?
the index.php script will only load the WordPress framework and run it, you need to add your js code in the theme/template files.
a little quote from the official word press site:
you can read more here
In my opinion, the best is that you should create a js file with the code you want to run and upload to your theme/template folder, and then add it with a script tag as the link i've provided explains.