I have the menu bar set at the top, then I have a script running under the menu bar that opens a a cart.
When I mouse over a menu item it hides behind the running cart script. How do I get the menu to "run" over the top of the cart?
Sometimes this behavior is dependent on where the menu bar code is actually positioned on the web page. Try moving the menu bar logic either to the bottom or top (opposite of where you have it now) so that it loads in a different order when the page is loaded. Sometimes this will fix the problem you are seeing.
Another option to try is to print some blank lines (using the HTML BR command) above the applet that is covering your menu option.