You're looking for the CascadingLoader:
// Mustache templates paths
$mustache_tpls = $_SERVER['BASE_DIR'] . '/views';
$mustache_override_tpls = $_SERVER['BASE_DIR'] . '/overrides';
// Mustache options
$mustache_opts = array('extension' => '.tpl');
// Mustache cache path
$mustache_cache = $_SERVER['BASE_DIR'] . '/tmp/cache/views';
// Cascading template loader
$mustache_loader = new Mustache_Loader_CascadingLoader(array(
new Mustache_Loader_FilesystemLoader($mustache_override_tpls, $mustache_opts),
new Mustache_Loader_FilesystemLoader($mustache_tpls, $mustache_opts),
));
// Init Mustache engine
$m = new Mustache_Engine(
array(
'cache' => $mustache_cache,
'loader' => $mustache_loader
)
);