Hi,
if I understood correctly what you were talking about, applying a template on APs through the controller launch pad applies it to all APs currently associated to a controller while selecting APs manually in the AP template launch pad applies it to selected APs regardless of the WLC they are on.\\
How do APs appear in the select list of the templates ? Simply by WCS knowing them, so usually by being associated to an WLC that WCS knows.
Nicolas