There is an example shortcut for config in the Maelstrom download, for ERAS. If you look at the properties, the Config Target: setting needs both the path to the Config.exe, a space, then the path to the mod you want to modify settings for, so it is a little different than using the Start In setting for the main game:
Target: C:\Maelstrom\gentlemen-of-fortune-maelstrom-engine\DirectX9_32bit\Config.exe "..\\..\\games\gentlemen-of-fortune-historical-eras-module-2"
Start in: C:\Maelstrom\gentlemen-of-fortune-maelstrom-engine\DirectX9_32bit
So in your case for ERAS, you could change it to:
Target: C:\Maelstrom\gentlemen-of-fortune-maelstrom-engine\DirectX9_64bit\Config.exe "C:\Maelstrom\Games\gentlemen-of-fortune-historical-eras-module-2"
Start in: C:\Maelstrom\gentlemen-of-fortune-maelstrom-engine\DirectX9_64bit