[Edit]

In the Header find:
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<!-- logo and buttons --> and highlight all until <!-- toplinks -->
-----------------------------------------------

And replace that with:
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<!-- logo and buttons -->
<center>
<table bgcolor=""#FFFFFF" background="images/mainbg.gif"" cellpadding="0" cellspacing="0" border="0" style="border: 1px solid #6597D9" align="center">
<tr>
<td>
<table border="0" width="750" cellpadding="0" cellspacing="0">
<tr>
<td valign="top" align="left" background="images/menu_background.gif"><a href="index.php?s=$session[sessionhash]"><img src="images/vBulletin_logo.gif" border="0" alt="$bbtitle"></a></td>
</tr>
<tr>
<td valign="bottom" align="right" nowrap background="images/menu_background.gif">
<!-- toplinks -->
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The above will make the buttons appear under the title image, aligned to the right.