steam is not this mysterious beast that you seem to think it is, the following can be used for all hl mods:
from the top (in game configurations), as i cant rememebr names and such =/ :
create a new config, like 'sci' for example, put in the appropriate fgd.
now down to the important stuff, the first line you can choose from (game .. something), click browse and search out the main folder for S&I, (psbly: C:/Program Files/Steam/Steam Apps/Science and Industry[whatever folder is called])
next line, (Mod Directory, i do believe), will be C:/Program Files/Steam/Steam Apps/Science and Industry/mod folder name (the folder with all the models maps and sprites folders in it)
third line is exactly the same as the top (C:/Program Files/Steam/Steam Apps/Science and Industry)
and Rmf Directory is your choice.
that's it.
ps, use batch compiler to compile, check the tutorial section for details..