All you have to do is read the SH3 Commander User Guide:
A common question raised through forums has been "will my Crew Manager changes be recognised within Silent Hunter III?". To answer this question:
· awarding *any* qualifications to officers impacts compartment efficiency as if they were awarded via Silent Hunter III;
· awarding the *first* qualification to a Chief Warrant Officer impacts compartment efficiency as if awarded via Silent Hunter III;
· awarding subsequent qualifications to a Chief Warrant Officer, whilst being recognised in Silent Hunter III, has no effect in Silent Hunter III;
· awarding a qualification to a Petty Officer impacts compartment efficiency as if awarded via Silent Hunter III;
· awarding a qualification to a seamen, whilst being recognised in Silent Hunter III, has no effect in Silent Hunter III;
· awarding any medal or badge has the same effect as if awarded via Silent Hunter III;
· promoting/demoting has the same effect as if awarded via Silent Hunter III (although there is no demotion via Silent Hunter III);
So, only qualifications awarded to seamen or extra qualifications awarded to Chief Warrant Officers are, despite being recognised in the game, not effective in the game.