1st.. Welcome Aboard Herr Kaluen!!
If I have a wounded merchant usually I hit F5 and follow him around on the map til I can line up a perfect shot.
I dont really see the need to have your periscope retracted when dealing with a crippled merchant. If for some reason they fire upon you submerged just lower your periscope in small incriments 'til they lose sight of you. Or drop it all together and just pop it up again after a little while.
As a rule, I don't waste my eels on anything less than 5k tons. Not very realistic I'm sure but I'd rather sink an Ore Carrier than a Tramp Steamer any day. Not to mention, If I hit a larger merhcant with 2 eels he is apt to
not linger as long as a smaller ship with but one hit. At least IMHO.
Hope this helps a little bit. You will find that each Kaluen here has there own skew on game play but in the end our goals are all the same.
GOOD LUCK HERR KALUEN!!