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:
When you add Css, you add it like this:
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.