Yep, external eels are stored in special compartments in between the exposed decks and the inner pressure hull. They've got to be moved inside the pressure hull for storage there or loading into empty tubes before they can be used.
In RL this was quite the operation as special equipment had to be set up on the deck in order for the men to hoist the eels out of external storage and angle them down through the torpedo loading hatches into the innards of the boat.
At sea in potentially unfriendly waters this would all be complicated by the added vulnerability of the boat to attack (particularly from the air) during the process.