If you are still looking for advice on qualifications I will give you my own for whatever its worth. I know many people may like to play differently so take whatever I say and adjust accordingly to how you like to play. This setup has served me well on a VIIB for my play style, it has a heavy emphasis on surviving.
What is the most important thing to you on your Uboat? For me personally, its making sure me and my crew return home. I cannot stress enough how important the Repair qualification is especially later in the war, always think ahead. Consider the worse case scenario, what happens when a DC or Mine goes off and you have heavy damage, broken machinery, heavy flooding, possibly multiple crew members dead (maybe one of them was a repair guy), and the ship is sinking fast when you are already at 100+ meters down? oh and maybe that destroyer or one of his friends is coming back around for another DC run at you. It may be overkill in some peoples opinion, but I like to give every main officer the repair qualification as one of his three qualifications, as well as 3 petty officers with the repair qualification. Within my game I have crew fatigue still enabled (a bit toned down though) and I like having the ability when I have damage to be able to throw any of the main officers into the repair station to have him greatly boost its performance. A main officer with the repair qualification along side 3 petty officers with repair will max out the repair performance bar! So there is your repair team for dire situations, and if needed, you can even add other random crew to it.
The next thing on my personal list of importance is what the Uboat is meant to do, Sink Ships. The second qualification for all but 1 main officer is Torpedoman, as well as 4 petty officers with torpedoman qualification. This is nice because when submerged you can toss a main officer and 2 petty officers with the torpedo skill into both the bow and stern torpedo rooms along side other crew, which will really cut down the reloading time of torpedoes. Now what about that one officer that didn't get the torpedo skill? This officer, whom will become your watch officer, will get the Gunner as his secondary qualification, to help improve the performance of the Deck Gun for the times you sink ships with the deck gun. Just him alone, with no crew at the deck gun station will make its performance over half way maxed, and even though he has gunner qualification, he almost maxes out the flak gun station even with no crew at it hehe.
The last qualification for each main officer is a mixed bag to help clean up all of the rest of the stuff that might possibly be needed. Starting with the odd ball dude who already has Gunner, and along side the importance of sinking ships, you first need to find them, so he gets the Watchman qualification. As personal taste, I also like to have 2 petty officers with the Watchman qualification to make sure the ability to see ships is at a max at all times. You can have both or just one on the bridge at a time for the unfortunate case you take damage while on the surface and one of them gets killed you will have an extra. Also, if fatigue plays a roll in your game, you can remove the main officer from the bridge when needed or also to just protect him at times while the two petty officer watchman keep the performance of seeing ships at a max. A situation where I use one or two of the watchman petty officers on the bridge without the main officer would be when I am passing through straights, or in areas with a very likely chance of getting spotted by destroyers or aircraft. The next 3rd qualification for two main officers, (usually I pick depending on the officers voice), is Helm. I think its nice to have two main officers with Helm as 3rd qualification, so that you don't ever run into problems not being able to steer the ship. Having two lets you swap one for the other to let one rest in bunk so they won't get fatigued badly. The next 3rd qualification goes along side having Helm officers, and that is to have one main officer with the Machinist qualification who (if needed) can help run either of the engines in emergency situations. Also have 2 petty officers with the machinist qualification who you will normally keep running the engines. I usually keep one in bunk the other at the engine station along side 4-5 crew members to keep its performance reasonable. Once they get fatigued from long hours, you simply swap all of them out for the same type of crew who are in the stern bunk, and you just keep alternating them throughout your patrol to keep the engines running. The last officer's third qualification I like to set to Medic, as well as having 1 petty officer as medic. I do this because you will normally always have an officer who is in bunk and having the medic qualification helps out the other crew in bunk i believe, then you toss the petty officer with medic into the other bunk. Also if one of your crew gets injured instead of having him die, you can put them in bunk with both the main officer and petty officer with medic, which will hopefully save his life. So that's it for the main officers and most of your petty officers.
To fill out the rest of your petty officers, I like to have 2 Radioman to help with the Radio/Sonar stations. Next, I like to make 1 petty officer Gunner to man the Deck Gun who along side the main officer with gunner will make its performance over max then you have the two extra crew as well who man the gun. I like to put one as Flak to help defend against aircraft, but 99% of the time when I encounter an aircraft I crash dive because I would like to make it to the end of the war if possible. Messing with aircraft is very risky and could end up getting many of your men if not all of them including you killed. The Flak guy is again for emergency situations when I may have low battery or oxygen, or possibly flooding where I have to blow ballast and am required to be on the surface and fight it out, aircraft or not.
These qualifications are not mentioned in order, it was a long process to get to this setup. I added what I needed at the time and ended up with this. Of course, this setup is not bulletproof and can have problems just like any setup. A really bad DC can end your career even with the best crew. In the end It is up to you as captain to make the decisions to keep your boat and its crew both operational and alive.
Hope this may have helped you in deciding what qualifications you decide to pick for your crew...
WolfyBrandon