I am not Chris, just one of his loyal servants haha.
The templates are definitely where you’ll need to be putting in the script, though it really depends on exactly what the script is.
Is the script in its own file? Something like fancy-content-slider.js? Or do you just have a block of code that you’re inserting into a template?
If it’s the former, hopefully you have a "header" PHP file (template) that you can simply add a link to the js. If it’s the latter, it might be a bit more tricky. Are you only wanting to add this to your main index page?