I think I may have found a way to use the cheat engine in the updated version of the game. First, you have to create two copies of the original (unmodded) installation folder. Then add the mods to one of the folders, open up the game, enter whatever cheat you want to enter, save, close the game and open it again but from the unmodded folder. The cheat carries over and there aren't any glitches (as of yet).