Source: http://www.prestashop.com/forums/topic/318418-solved-center-logo-in-new-theme-16/
open header.tpl file (located in your theme dir) and remove this code:
<div id="header_logo"><a title="{$shop_name|escape:'html':'UTF-8'}" href="{$base_dir}">
<img src="{$logo_url}" alt="{$shop_name|escape:'html':'UTF-8'}" width="{$logo_image_width}" height="{$logo_image_height}" />
</a></div>
then go to /themes/default-bootstrap/modules/blocksearch/blocksearch-top.tpl and paste code that you removed at the end of the file
Possible issue: This edit may affect the responsive layout, leaving the logo in the middle of the screen in between Search block and Cart block.