depends on what you want to do but on one of my sites that uses flash as it's navigation (
http://www.hom.gb.com/shop/
i just made a php file with the code that usually occurs when you insert flash into a page with dreamweaver, saved that and then used
{include_php file="topnav.php"} to insert it into the head.tpl
other than that there is a module on
http://www.cart-lab.com for using flash in x-cart