I was needing to do basically the same thing as my logo was too tall and it took up too much real estate at the top of the page. In my case moving the top links over the logo was just to help everything move up a little. It looks much better now.
I have a couple of notes to add however. I had to make some additional changes as this worked wonderfully in Firefox, but broke in IE6. In IE6 the page was shifted down by only the amount the nav links would normally push down to the logo. Then there was a space the height of the logo that was white and covered the bottom of the logo to the beginning of the rest of the page. To make it look the same in both browsers I basically moved the height attribute to the headerWrapper ID and totally eliminated the logoWrapper from both the style sheet and the tpl_header.php file. meaning that I have this in my stylesheet:
/********************************************************************/
/******************** Header nav over logo mod ******************/
/********************************************************************/
#headerWrapper {
margin: 0em;
padding: 0em;
background-image: url(../images/logo.gif);
height: 199px;
}
#navMainWrapper {
margin: 0em;
background-color: transparent;
padding: 0.5em 0.2em;
font-weight: bold;
color: #ffff00;
height: 2em;
}
/********************************************************************/
/****************** End Header nav over logo mod ****************/
/********************************************************************/
and I completely deleted the logoWrapper div and everything in it. It worked like a charm.