Can anyone tell me the name of the movie where in one scene the sailor sews marbles into his captain's abdomen

Ensign Pulver (http://www.imdb.com/title/tt0058060/). It's sort of a sequel to Mister Roberts, only with different actors in the key roles.

The only 2 navy comedies I know is...
McHale's Navy
You're in the Navy Now

But I don't recall the marble seen in the re-make of McHales Navy (Tom Arnold stars in it)

Ensign Pulver, it was a sequel to Mister Roberts