Whilst googling and trying to answer my own query I came accross this thread
http://www.uboat.net/forums/read.php?3,78865,78887
Which details the whole procedure of loading torpedoes into a type IX, which I found fascinating.
Especially this picture which shows them shoe-horning a torpedo into an external bay using a special cradle.
Notice the guy on the right is standing on a winch, which in turn is resting on a stool - no health and safety back then lol.