To get your guys on ships, I recommend building a dock or pier out to sea. If that doesn't work check and see if your troops can go in water in the first place.
As for the submarine, I can't remember if I ever had problems with it. The only time the sub moves (if I recall) is at the end of the last Russian mission. Other then that it just stays there.
I had a problem with the Italian destroy as well. Only the vitals of the ship can be destroyed, but never sunk. The destroyer was only used in the last German mission. I don't think it ever does sink there.
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