Greetings Sanctuary, I myself have only been playing SH4 for about 5 days and doing the same as you, trying to get all my answers on the forums. Tried looking around to answer your question and found this on another forum created by Tambor198.
DAMAGE CONTROL
1. If you play long enough, you are going to take damage. From reading through the posts since the game's inception, it seems that a fair number of skippers aren't too sure what to do when that happens.
2. Before you go on patrol, make sure that all of your damage control team slots are full. Yes, you can pull a damage control team together from other compartments if you want to, but why? It's not like the game is going to reduce your crew's oxygen consumption if you have less men on the boat. Pick at least one chief petty officer, fill the other slots with guys who have engine (propeller) qualifications. Get the green status bar on the left as close to the top as you can. And when you are handing out promotions and medals, not a bad bunch of guys to keep happy and efficient.
3. If you take damage and you haven't done so already, A) send your crew to general quarters. This activates the damage control team, and at least in theory allows them to utilize the regular crew in the compartments as well. B) Secure from silent running. I don't know if that mode keeps repairs from being made, but why chance it.
4. What to pick from the damage control list? Well, that's your call, but I tend to put things into a couple of broad categories, going from most important to least important:
1. Survivability
2. Maneuverability
3. Everything else
Survivability, fix leaking bulkheads, make sure my main pump is intact to pump the water out, and that my compressor is working so I can surface. Also, the amount of blue in the gauge on the right shows how badly the bulkhead is leaking. The more blue you see, the higher on the list I would put it. Blue in the compartment indicates how much water is in there. Again, more blue is bad. Fix the worst flooding first.
Maneuverability, diesels, electric engines, batteries, props, dive planes and rudder. If I get through all the stuff above, I'm going to need these.
Everything else, as the name implies, is just that. If I've taken any sort of major damage, I'm not attacking anything anymore. Why worry about my attack periscope, or my deck gun when I plain to dive if I see so much as a seagull checking me out.
And keep in mind, that some items (such as deck guns) an only be repaired when you are on the surface.
3. While you are trying to get flooding under control it may be necessary to increase your speed to keep from sinking below crush depth. And keep in mind that if you are taking on water, crush depth is a lot less that it used to be. I try not to run flat out at a sustained speed, unless I have already sunk the one escort that was in the area. Otherwise, crank on the speed and move towards periscope depth, reduce speed when I get there so my batteries last, and hopefully sink slowly back down. Repeat as necessary.
4. If your batteries took damage be very careful. If and when you get back to the surface watch your battery status bar to make sure you are getting a charge back in the batteries. If you are, be sure they recharge to 100% (wait for the text message). If they don't turn battery charging off when they've taken all they can or you will suck up fuel like there's a hole in your tank.
Hope this helps you with damage control.