U-Boat Command Structure...
 

A couple questions...

Who was the Executive Officer of the boat? Now, I'm referring to Das Boot somewhat here, was it the IWO or the Chief? And also, was that most likely the IWO in the beginning shouting while the Captain, Chief and Leutnant Werner were walking to the boat? I beleive he said something like "Der kommandant kommt! Auge... Links!"

I think this is where Das Boot was showing the disconnect between the 'official' German structure and reality. In the movie the tight ass first officer, although next in command based on official doctrine, did not have the captain's confidence, like that afforded the chief engineer.

Whether or not this existed throughout the U-Boat service may be up for debate, but that is how I perceive the differences in Das Boot the movie.

EDIT: There are other examples in he film where 'official ' doctrine is openly questioned. 'Geohring that fat pig' , the 'Tiparary song if you please' etc.

Yes, the 1WO was second in command. As with the British Royal Navy, the Engineering section was separate from the Command line. The Chief was the go-too guy, but officially was not qualified for command.

In Das Boot, the IWO always seemed like a noob to me. Wouldn't he have been more seasoned?

If it's anything like real life, rank is not a measure of experience and competence - It's a measure of certification and brown nosing abillities.

After watching the extended, 5-hour version (many times), I came to see him less as an untrained party member and more as a young man who's a joiner - he wants to be liked so he tries to be like what he thinks a good officer should be. As for being a noob, one thing I've noticed is the attack scenes: whether they are the attackers or are under severe depth-charging, he is always calm and does his job well. He may impress most of his comrades as a jerk, but he gets underestimated as an officer.

By mid-war, U-boats were being produced like sausages, as were their officers. Officers may come in new as the Second Watch officer. If they survive even a patrol or two they are already First Watch. Captain is maybe another two patrols away. When 23-year olds (Leupold) can make Captain, you can see how green the IWOs will be.