There is an XML configuration folder located in app/design/frontend/PROJECT/THEME/layout. The main one is called page.xml. Within there, you add JS resources you do it like this:

<action method="addJs"><script>madskull/cookie/jquery.cookiebar.js</script></action>

When you add Css, you add it like this:

<action method="addCss"><stylesheet>css/styles.css</stylesheet></action>

Magento does some stuff in the background and auto tries to put you in the /js dir. There is a third way called addItem:

<action method="addItem"><type>skin_css</type><name>css/styles-ie.css</name><params/><if>lt IE 8</if></action>

You can say skin_css or skin_js, and it will set the path for the module.

Apparently, adding files stored in say bower_components just won’t work. The solution is either to hardcode the html into the head.phtml file (which they dont recommend), symlink the bower library to the JS folder you require, or just dont use bower and copy it straight in to your theme. lternatively, there is a class written by some guy that extends Mage_Page_Block_Html_Head. He hasn’t put it on Github, which I’m  uneasy with (I like stuff on Github and versioned!) but in the meantime you can get it here