Selectively Loading Javascript files by page?

Just use a conditional tag that suits your purposes. For example in functions.php:

function my_scripts_method() {
	wp_enqueue_script(
		'custom-script',
		get_template_directory_uri() . '/js/custom_script.js',
		array('jquery')
	);
}
if(is_page( 'Foobar' ) ) add_action('wp_enqueue_scripts', 'my_scripts_method');

will only load custom_script.js on a page with the title “Foobar”.

You should always enqueue your scripts in a theme’s functions.php file – not a template file. Template files are just Not The Right Place 99.9% of the time. The add_action is needed because the my_scripts_method() function won’t run unless something calls it. wp_enqueue_scripts is a core hook specifically designed for scripts that runs very early in the page load and fires off any functions that have been added to it.

is meant to be included in the -template- PHP file, right?

No. All of the code I posted just above should go in your theme’s functions.php file.

Am I missing the sequence of when functions.php is loaded?

functions.php is one of the very first things that WP loads on every single Post, Page or archive. Certainly the very first file from your theme. So you can use it to load all kinds of cool stuff and make that same cool stuff conditional.

To work properly, scripts need to be enqueued at the right time during the page load. If they’re loaded too late they may not work at all. So you need to hook them to the wp_enqueue_scripts action.