I haven't tried, but likely not. What would the new directories be for? You mean like making one with a mod name, and just having all the relevant files in there instead of distributing the mod files over several core folders?
Yeah, like I would create a directory - say - \My Games\Elemental\Ironmana_Mod. Then I could put my customized files in there - instead of throwing them all in the "Units" directory which just seems...kinda wrong. I mean, why is my tweak sound file in the Units directory. It's not a unit - but it has to go there so it can get seen by the game. Seems like it would get really confusing and chaotic.
Of course, I guess it couldn't work because the game can't know they are there. That's one reason I'd like some kind of mod manager or something where we can set what mods we want to play with, but at the very least, being able to tell the game where directories are so we can organize multiple mods would be very helpful.