Anyway to add a Mod on a Steam account?

[Painboy]

As an experiment I decided to but M2TW off of steam (and probably the last time I will buy a game that way). However when I try to install mods into the correct folder the mod will not start up correctly. Gives me an error message saying it can't find steam. Any way around this? This looks like a really good mod and I'd be willing to manually overwrite things if I have too.