for each menu that is created, a separate folder is created. the naming convention is:
CSSMenuWriter/cssmw<int>
where <int> is a number starting at 1 and incremented for each new menu.
inside the cssmw<int> folder, open the menu.css file. add the z-index to the first style:
ul#cssmw<int> {
cursor: default;
list-style-type: none;
margin: 0 0 0 0;
padding: 0 0 0 0;
position:relative;
z-index: 1;
}
set the z-index higher for the menu you want to appear on top.