I helped someone getting two emulators playing Pokémon at the same time - I guess the same principle applies, but it's not straight forward. You would have to create a script for each selection of roms that you want to play at a given time, in advance. Meaning, that if you want to change roms every time you play, you would have to alter the scripts. Also, the emulators need to support background input from the controllers, for it to work. Meaning, the window doesn't have to be active, for it to receive input. Honestly, I think it's actually more easy to just do it manually, as Jason said.