Arracing - You should modify your index_header template as Faranth suggested, but if you copy your normal header be sure to add $bburl in front of each of the links, otherwise they'll be broken.

As far as the queries, if you'd like to put your server in debug mode (Add $debug=1; somewhere in your admin/config.php file), then go to the url
http://yoursite.com/index.php?explain=1
If you'll do that and post the results here I'll see what is causing the extra queries.