Welcome to the boat mate.
In my experience it's not necessary to line up the waterline but I find it helpful to do so, I seem to get better results that way. I try to do everything exactly the same every time.
Opening the torpedo doors, setting torpedo speed and depth and exploder etc well ahead of time, depth at 15'. That will sink most all merchants and even many warships, you can always reset things later if necessary but you'll not forget to do so in the heat of battle. Nothing worse than missing or doing little damage because your fish were set to slow speed or 5 feet or the doors weren't open
A couple of things about using the TDC/PK shooting method.
When using the data entry tools always input the data in this order.
Turn on the PK.
Input Speed first.
Input AoB next and
Last thing is range and bearing.
It will make a difference.
Magic