As a solution I've ended up compiling the files directly from the scss forlder and I now have there the main config.rb I still would like to have control about where the config.rb is and the subfolders that are getting filled in the compilation process.
If anyone has a way to better control this, please let me know.
The other thing: "to compile just a few of the scss files"
The way to do this is to rename the files you don't want to be compiled starting with underscore _print.scss (instead of print.scss). The good thing is that you can still import the files as you normally would, without the underscore (even if the actual file has the starting underscore)
@import "print.scss"