It means you would type "NoMariosSky.exe -resetPrefs" without quotes in the command line at NoMariosSky.exe's path. "NoMariosSky.exe" is the command and "-resetPrefs" is an argument that the command understands. Hope this also resets your controls.
Strange that it didn't reset the controls. The settings are stored in the registry in HKCU\Software\ASMB\No Mario's Sky so you could delete that registry key. We'll look into it!
