The background-dimming overlay has z-index: 11100, and the actual cart display has z-index: 11102. You should be able to override these with !important CSS declarations like so:
EJEJC_overlay /* background dimmer */
{z-index: 12200 !important;}
EJEJC_window /* cart display */
{z-index: 12202 !important;}
BTW, if your actual problem is that Flash content in your page (e.g., embedded video) always shows up in front of the cart, that's not a z-index issue; you need to set Flash content to be "transparent", so the cart can show through the Flash:
http://www.e-junkie.com/ej/help.flash-shopping-cart.htm
http://www.e-junkie.com/ej/tips.flash.youtube.htm