Look in the CSSMenuWriter\cssmw_home\menu.php file.
do you mean the common.css file? if so, change this code to use another css file:
<style type="text/css" media="all">
<!--
@import url("../store/css/common.css");
#outerWrapper #navWrapper {
padding-bottom:0px;
z-index:999;
}
-->
</style>