Bootstrap subtheme does not apply to main menu
You must use the template files from bootstrap theme since all those are overridden there. the templates file you should use are under themes &gt; bootstrap &gt; templates &gt; system. 

copy the page.tpl.php and html.tpl.php from there to your sub-theme.

simply use the same .info file for your sub theme as well. it will give you all the regions. set "base theme=bootstrap" in template_name.info file.

remember to clear the cache