In version 2, your portal HTML must be in the
custom/templates/*template*/portal.tpl file.
You can add any custom CSS into the custom/templates/*template*/css/custom.css file, and images can be uploaded anywhere but make sure that if your CSS refers to any custom images that the paths match.
Javascript can be added into custom/templates/*template*/template.php file, within the
$js variable which starts on
line 45.