Well I am telling this from memory so...
Open the program, and depending on where your game is (I assume it's in C:/ ) type "MOUNT C: C:/" and the emulator will allow you to access the drive. Open the game folder with the emulator (e.g. "cd GAMES" ) and you will open the C:/GAMES folder. You can type "dir /p" to view all the folders and objects within one map. Once you find your game all you need to do is type "Start.exe" or whatever the executables name is to run it. You might want to adjust the CPU usage and frameskip with F1-F12.