I just use Neko Project II's ini files as my roms. Everytime you load a game in Neko Project it updates the default ini file. I create a copy of the ini file for every game. The ini files are now my "roms" which calls the real roms.
Also use -f if you want to run the games in full screen right from the start.
executable: np21nt.exe -f
The solution requires you to create an ini file for every game. This is not really a bad thing, since some games need its own emulator settings. You get to check if the game is working with your emulator setting. A good example is Touhou 4. Touhou 1-3, 5 works fine using the recommended setting from the website I downloaded the emulator. But Touhou 4 needs a slower CPU multiplier, for most users and me.