Been tinkering with it today since I had a little bit of time. In order for your cmd line to work, I had to take the contents of the bin folder, and place it in the root of the emulator folder. It doesn't override anything or make changes to the file structure, that i've noticed anyway. After the contents where added to the root, change the working path to the root folder. Then the cmd line of gcube.exe -f "[ROMPATH]\[ROMFILE]" will work. For some reason it won't read any of my game iso files, only gcm.