Which file to add code to load javascript

I want to add an external javascript. WP documents said I either need to add code in header.php or add code in functions.php.
I find out I have header.php in each of the 2 themes that comes with WP, but in the theme that I currently use, there’s no header.php.

So, now I try the 2nd method, to add code in functions.php, but I find that beside one in includes folder, each theme folder has one functions.php.

Which functions.php is the file I should add the javascript code?

Thanks for helping!