Q:

How do I overlay a menu ontop the rest of my site?

I have php generating html and I want to create layers.  Basically I want to have a menu overlay without messing up the structure of everything displayed under it.

A:

Try this:
CSS:
#menuOverlay {
   position:fixed; /*or  absolute*/
   top:0;
   left:0;
   width:100%:
   height:30px;
   background:green;
   z-index: 999; /* or  greater value */
}

HTML:
<div id="menuOverlay">
   menu items here ....
</div>

