Did you download the manual and read the instructions?
Here they are from the manual
Installation Methods
The NYGM Tonnage War mod may be installed by two different ways. As with any
modification to the stock game, it is highly recommended to make backups of all
important information prior to installation of this or any other modification package.
Method 1: Manual Installation
Extract the 7z archive(s) to a convenient location, then copy the included files to your
X:\Program Files\Ubisoft\SilentHunterIII\data folder (where X is the drive with the SHIII
installation, usually C:)
Method 2: JSGME Mod Installer
For most people, this is the preferred installation method. Simply extract the 7z
archive(s) to the MODS folder and install. In order to get the full benefit of the NYGM
Tonnage War package design, it is highly recommended you upgrade to the latest version
of JSGME. The latest version can be downloaded here:
http://members.iinet.net.au/~jscones@iinet.net.au/software/products.html