MAP files are generated by GameEx in the DATA folder of your GameEx install based on the files in the rom directory. So in your case, prune out the games that are not used by that emulator and paste them into another map file accordingly and also save the edited one as a different filename. The files are named EMU_#.map, # being the emulator number slot in Setup Wizard. To use one that is created by a user or yourself, simply point to it in the Advanced Emulator Setup section, setting MAP File in Setup Wizard.