I just finished skinning most of my whmcs install and it's coming along nicely. Instead of trying to integrate whmcs in my site, I just decided to skin whmcs and add a few custom pages, since my site is not very content heavy. I wanted the index page to be a custom page, so i just created a new custom page called 'Client Panel' which is an exact copy of the homepage.tpl. Homepage.tpl will be an introductory page which should not have the whmcs 'look' to it (only my skinning done in the header).
On these 'custom' pages, I don't want footer.tpl to be included, nor do I want anything in the 'content_container' div to be displayed. So, I am looking for a way I can ignore the automatic inclusion of the whole footer.tpl and specific divs within header.tpl