They were stored in waterproof containers mounted to the outside of the pressure hull top, inside the outer hull. The retrieved them by actually setting up a loading hoist, lifting the container out on a tilt, and pulling the torpedo, warehead and all, out of the container, and down the loading hatch. The type IX had rails on which the torpedos could be rolled on for removal and loading, so ones stored in the front of the boat could be sent to the stearn, and vise versa. (Sh3 and Sh4 UBM got this wrong with the type IX, and limit where you can have the reserve torps loaded.) This was done at sea, at very slow speed or hove to. The seas needed to be quite calm as well.
If you think that is something look at a picture of a torpedo being transfered from one boat to another. Quite something.
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