Hi, currently in the theme you provide 2 optiontion for CSS.
1.Entering custom css as internal css
2. or to insert a custom css file as external css
But for JS you just have only 1 option, i.e insert custom js files as external js. There is no way to insert js functions as internal js (like the css) and also make sure that the js functions load in wp_footer, because adding them in wp_header will cause serious site load time issue.