this is an example of how I solved this with a theme function…
function do_include($file)
{
$parent = get_template_directory() . '/';
$child = $parent . '../' . get_child_folder() . '/' . $file;
$parent = $parent . $file;
if(file_exists($child))
include($child);
elseif(file_exists($parent))
include($parent);
}
function get_child_folder()
{
return array_pop(explode('/', dirname(get_bloginfo('stylesheet_url'))));
}