The first step with the Ctrl+M cheat is that you must modify the game's startup shortcut:
"C:\Program Files\Stardock Games\FallenEnchantress\FallenEnchantress.exe" cheat (as an example)...note the 'cheat' at the end of the executable line (accessible under the general tab under Properties).
This is exactly the same as for the earlier version of Elemental.
Start the game as normal, and Ctrl+M should work...at least it does for me, even with the Cheat Happens trainer also running. They seem to work together smoothly.
Instead of just having a Super Unit Function that sets the level to 9999, is it possible to change it back to the original game's trainer stat editor? Where you can set the individual stats as oppose to a across the board boost?