Back in the day the trick to get SweetFX working was to split up the files manually into different directories. I have no idea why this was required but wanted to pass it along as it might help for future versions of "ReShade Setup.exe."
That's because InjectSMAA loaded files from the current working directory, which is not guaranteed to be the one the executable or DLL is in (game can change it). ReShade on the other hand always loads files from the directory its DLL is in, so that issue should not be present.
So it should be fine to install everything into "SC2\Versions\Base" ...