1) The Specials listing doesn't change no matter which option I select in admin. Is there a trick to this one?
No trick. But the Specials listing does work differently to the others.
Check all the files have uploaded correctly.
2) Is there anyway to set the index listing to use the common template
That should be option 2.
Enable the Template Debugging and see which files are being used. Option 2 should have
FUNCTION index_listing in \includes\functions\extra_functions\index_listing.php

shown above the listing with option 2.