When you're in port you can drag and drop your torp loadout to whatever you want.
If out at sea, as stated turn autoload off and load them as you please. Why at sea, with autoload off you can unload tubes by dragging loaded torps to an empty tube if you have an empty rack. This is also helpful is you get a damaged tube, you can unload the torp and use it in a good tube if you have one.
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