Apart from the mods/fixes you need to exercise some patience. Use TC for crossing the wide expanse of the ocean primarily. Do NOT use TC when you are in harm's way (as you found out). TC compresses a lot more than just time if you use it carelessly.
Your sub operates best by stealth and surprise, lose that and you pay a price. There are many posts on tactics etc which will help you become a better skipper.
As mentioned, get away fm the vanilla game as soon as you can and get one of the superb mods (TMO or RFB) combined with RSRD. You'll appreciate the difference.