It's always much easier to get everything you need right in Photoshop, huh? You can fix the overlap issue with two minor CSS changes:
styles.css
#top {
position: relative;
z-index: 2;
height: 155px;
}
ddsmoothmenu.css
.ddsmoothmenu{
position: relative;
z-index: 2;
}
homerotation.css
div#feature_list {
position: relative;
z-index: 1;
}
, z-index: -100, CSS. . 2 .
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Edit
z- #top, <div>, <div id="feature_list">.