The external reserve torpedoes are in a special 'well' under the deck. A small crane is rigged to take them out of the well. They are placed into the boat via a specialized torpedo loading hatch.
http://img64.imageshack.us/my.php?im...itled317dz.jpg
http://img64.imageshack.us/my.php?im...itled322pp.jpg
These pictures were taken in port, so of course they are being loaded using a larger shoreside crane, but you can see the hatch clearly.