It doesn't really matter. Just start the macro before starting the game, Before SH3Commander or before you click start in sh3commander. If you forget you could also just ALT-Tab and start it while the game is running.
Set "AutoStartSH3 = 0" in the .ini file with notepad so not to start the game without SH3commander.
When finished playing exit the macro by right-clicking on it in the system tray.
Note:
The CTL+ALT+v config should only need to be done once or when changing Gui, mod, resolutions etc.
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