1) install the game (desktop icon points directly to WorkaroundLauncher"StartShogun2.exe")
2) Apply Crack
3) Run the game - select option 2 (game needs to be runed at least once to create blank gamesettings file) and LAunch in ModManager
4) Quit the game and inside Launcher window - click any key

for game setting change there are 2 options inside launcher (ingame ones doesn't save between game sessions):
0 - copies preset gamesettings file (on ingame Medium settings) file to location which game reads
1 - opens game-settings file in notepad for editing (you can set settings you want and game will read that - its even nicely decribed what which line does)
BTW: the ettings file is preferences.script.txt in "%appdata%\The Creative Assembly\Shogun2\scripts"