They need not show in the homepage BUT only if you've chosen to use only a section of the site. E.g. http://www.mydomain.com/section Weight will be given based on the PR of the root page. http://www.mydomain.com/section in this case. All pages below the root page should have coop ads. For most people the root page is their homepage so for them all pages on the site should have the coop ad - even if they are not php. You can find instructions to set up the non-php pages in maybe the FAQ.