I think you can put it in the game folder and run it or just drag the game exe over
aw2-cmdline-standalone.exe
I havent tested myself as i no longer have the game installed but this is what it says:
[19:01:02] [info] [cmdline-standalone] Test!
[19:01:02] [error] [cmdline-standalone] File "C:\Users\me\Desktop\AlanWake2.exe" does not exist, cannot patch
[19:01:02] [info] [cmdline-standalone] Usage: C:\Users\me\Desktop\aw2-cmdline-standalone.exe [path to AlanWake2.exe]
[19:01:02] [info] [cmdline-standalone] Or drag and drop AlanWake2.exe onto this executable
Press any key to continue . . .
Edit: And i think after patching you should add the args in a shortcut of the game exe