what you need to customize a mod,block or a theme...?
here is the method you can use to add js and css in your plugin:
css folder and javascript folder (js) should be created inside that plugin(mod).
below syntax should also be included to add style and javascript in view.php page of that plugin.
$PAGE>requires>js(new moodle_url('/mod/modname/js/jquery.min.js'));
$PAGE>requires>css(new moodle_url('/mod/modname/css/style.css'));
$PAGE>requires>js(new moodle_url('/mod/modname/js/javascriptname.js'));
( jquery.min.js file should be kept under js folder.)