Alternative Menu Items are used and work the same way as standard menu items. Since they are already based on customised layouts, template overrides do not apply to alternative menu items.

A Cascading Style Sheet or CSS is used to control the presentation of an XHTML page. For example, a CSS file will often control the font, margins, color, background graphics, and other aspects of a web page's appearance. CSS allows you to separate the content of an XHTML page from it's appearance. In Joomla!, CSS files (for example, template.css) are normally part of the template.

Reference: http://docs.joomla.org/Glossary