Remember that Grey Wolves and NYGM Tonnage War are completely seperate mods and cannot be used together.
As for the waterline thing, I think that's a typo. Shots other than the waterline will do little. You really do want to hit the waterline mostly to help areas flood, leading to sinking.
Again, NYGM Tonnage War and Grey Wolves are seperate "supermods" and you can't install them on top of each other. You can have seperate installs of them (two copies of SH3 one with GW, one with NYGM).
You can use SH3 Commander with either mod, just remember to rollback changes before using the other mod just in case.
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