The schnorkel is on the starboard side, it's base is anchored to the SB side and just forward of the conning tower. The snorkel runs about 40 feet (@13 meters) forward of the conning tower, on SB. I looked at it in game, and from what you were explaining, I think the schnorkel cover is what you are speaking of. When you do get the schnorkel, that cover will be removed. You can always go into single player and use a late war u-boat and find a quiet spot to check it out.
