I was trying to not use the site's default layout template for a popup iframe (using fancybox), as I didn't need headers/footer information.

To do this, create a new template file called, for instance popup_pagelayout.tpl

and in the link to your view, use prepend the following: "/layout/set/popup/" to your existing "module/view". What this does it tell EZ that you are using the popup template file, then it continues to execute your module as before.