To control the formatting of the source code you will need to make updates to a few pages in the site, you can do all of the changes at once with a global find and replace, here is a post with the details of what to look for and what to update it with.
showpost.php?p=60090&postcount=9
in your original post were you referring to the format of the source code or did you mean that extra code you didn't want was being included? Let us know if there is still a problem and we will look into with you.