First off, the so-called 'Crew Management' in SH3 has nothing to do with real life. The crew are organized into rotating 'Watch Lists' and trade themselves out after two, four, six or eight hours, depending on the navy, the ship and the job. SH4 fixed this so it works much more realistically, but in SH3 this is seemingly impossible. The captain moving the crew around whenever they complain about being tired is just not the way it works. Commander allows you to turn off fatigue altogether, which in this case is the most realistic, unless you like moving the crew around yourself.
@ Aras: I too use Commander to qualify my crew. After a 'False Patrol', in which I make a tour of the harbor and then dock again, I qualify all my petty officers on the grounds that being qualified is what gets them called 'petty officers' in the first place. We had an interesting and educational discussion on the subject in
this thread .
Qualifying your non-POs doesn't affect their abilities but it does let you remember who you assigned where.