Since the official PPSSPP is now supports multiple instance on one PC, may be someday they will have a separated controller config for each instance.
You can try requesting this feature/option on github if it's not already there
You can try requesting this feature/option on github if it's not already there
PPSSPP Multiplayer Guide: https://github.com/hrydgard/ppsspp/wiki/How-to-play-multiplayer-games-with-PPSSPP