If you are willing to get into romhacking, you should learn how to use command line tools as it's one of the most basic things.
Put the exe and the fa on the same folder.
Hold shift and right click on the white part of the folder window and select "open command window here" or something similar. A black window will open (cmd).
Write the program name followed by the fa name. For example myprogram.exe myfile.fa
or just open a cmd and cd your way to the proper directory.