Sure, you can add html to the 'Configure Header Options' so remove the %logo and replace it with
HTML Code:
<div id="logo area">
<div valign="middle" class="logoarea-logo">
<a href="http://globalstudiesrap.colorado.edu/">
<img class="logo" id="mainLogo" src="http://globalstudiesrap.colorado.edu/wp-content/themes/atahualpa/images/banner_white.png" alt="Global Studies RAP" />
</a>
</div>
<div id="searchBox">
<div id="culinks">
<strong>CU:</strong>
<a href="http://www.colorado.edu/">Home</a> •
<a href="http://www.colorado.edu/">A to Z</a> •
<a href="http://www.colorado.edu/">Campus Map</a>
</div>
<form action="http://www.colorado.edu/search/custom/searchdirect.cgi" method="post">
<input type="hidden" name="searchtype" value="http://www.colorado.edu/" />
<input id="cusubmit" type="text" class="text" name="searchstring" placeholder="Search this Site..."/>
<input id="cusubmitbutton" type="image" src="submit.png" value="Submit" border="0" />
</form>
</div>
</div>
you do need to use a fresh copy of bfa_header_config. php and you still might need to tweak the positions, but there you go, and now it it is part of the theme options